1
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Role of oncogenic KRAS in the prognosis, diagnosis and treatment of colorectal cancer. Mol Cancer 2021; 20:143. [PMID: 34742312 PMCID: PMC8571891 DOI: 10.1186/s12943-021-01441-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease at the cellular and molecular levels. Kirsten rat sarcoma (KRAS) is a commonly mutated oncogene in CRC, with mutations in approximately 40% of all CRC cases; its mutations result in constitutive activation of the KRAS protein, which acts as a molecular switch to persistently stimulate downstream signaling pathways, including cell proliferation and survival, thereby leading to tumorigenesis. Patients whose CRC harbors KRAS mutations have a dismal prognosis. Currently, KRAS mutation testing is a routine clinical practice before treating metastatic cases, and the approaches developed to detect KRAS mutations have exhibited favorable sensitivity and accuracy. Due to the presence of KRAS mutations, this group of CRC patients requires more precise therapies. However, KRAS was historically thought to be an undruggable target until the development of KRASG12C allele-specific inhibitors. These promising inhibitors may provide novel strategies to treat KRAS-mutant CRC. Here, we provide an overview of the role of KRAS in the prognosis, diagnosis and treatment of CRC.
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2
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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3
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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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4
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Meng M, Zhong K, Jiang T, Liu Z, Kwan HY, Su T. The current understanding on the impact of KRAS on colorectal cancer. Biomed Pharmacother 2021; 140:111717. [PMID: 34044280 DOI: 10.1016/j.biopha.2021.111717] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS (kirsten rat sarcoma viral oncogene) is a member of the RAS family. KRAS mutations are one of most dominant mutations in colorectal cancer (CRC). The impact of KRAS mutations on the prognosis and survival of CRC patients drives many research studies to explore potential therapeutics or target therapy for the KRAS mutant CRC. This review summarizes the current understanding of the pathological consequences of the KRAS mutations in the development of CRC; and the impact of the mutations on the response and the sensitivity to the current front-line chemotherapy. The current therapeutic strategies for treating KRAS mutant CRC, the difficulties and challenges will also be discussed.
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Affiliation(s)
- Mingjing Meng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Keying Zhong
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ting Jiang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
| | - Hiu Yee Kwan
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Tao Su
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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5
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Kuroda K, Yashiro M, Miki Y, Sera T, Yamamoto Y, Sugimoto A, Nishimura S, Kushiyama S, Togano S, Okuno T, Ohira M. Circulating tumor cells with FGFR2 expression might be useful to identify patients with existing FGFR2-overexpressing tumor. Cancer Sci 2020; 111:4500-4509. [PMID: 32946655 PMCID: PMC7734156 DOI: 10.1111/cas.14654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
Fibroblast growth factor receptor (FGFR) is associated with proliferation, migration, and angiogenesis of carcinomas, and FGFR signaling inhibitors are considered a key drug for the treatment of solid tumors with FGFR overexpression. Amplification of FGFR2 is reportedly identified in 3%‐10% of gastric cancers (GCs). The aim of this study is to clarify whether the identification of the circulating tumor cells (CTCs) with FGFR2 overexpression is useful to detect patients with FGFR2‐overexpressing GC. One hundred GC patients who underwent gastrectomy were enrolled. A total volume of 8 mL of peripheral blood was collected from each patient just before gastrectomy, and mononuclear cells were enriched by Ficol density gradient centrifugation. These cells were immunostained with PI/CD45/EpCAM/FGFR2. The number of CTCs with FGFR2 expression in each sample was enumerated by FACScan. The FGFR2 expression level of the resected primary tumor was assessed by immunohistochemistry. The number of FGFR2‐positive CTCs in the GC patients' peripheral blood was significantly correlated with the FGFR2 expression level of the primary GC. The relapse‐free survival of the patients with FGFR2‐positive CTCs (≥5 cells/10 mL blood) was significantly poorer (P = .018, log‐rank) than that of the patients without FGFR2‐positive CTCs (<5 cell/10 mL blood). These findings suggested that the determination of FGFR2‐positive CTCs might help identify an existing tumor with FGFR2 overexpression.
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Affiliation(s)
- Kenji Kuroda
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masakazu Yashiro
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yuichiro Miki
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Tomohiro Sera
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yurie Yamamoto
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Sugimoto
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Sadaaki Nishimura
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Shuhei Kushiyama
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Shingo Togano
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Tomohisa Okuno
- Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan.,Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.,Cancer Center for Translational Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masaichi Ohira
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan
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6
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Matsumoto K, Kato H, Nouso K, Ako S, Kinugasa H, Horiguchi S, Saragai Y, Takada S, Yabe S, Muro S, Uchida D, Tomoda T, Okada H. Evaluation of Local Recurrence of Pancreatic Cancer by KRAS Mutation Analysis Using Washes from Endoscopic Ultrasound-Guided Fine-Needle Aspiration. Dig Dis Sci 2020; 65:2907-2913. [PMID: 31897893 DOI: 10.1007/s10620-019-06006-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The sensitivity of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) for diagnosing the recurrence of pancreatic cancer is usually low because of difficulties in obtaining adequate samples for pathological examinations. We evaluated the efficacy of highly sensitive KRAS mutation analysis using EUS-FNA washes to detect cancer recurrence. METHODS Nineteen consecutive patients with suspected pancreatic cancer recurrence after surgical resection were enrolled. All underwent EUS-FNA, and samples were obtained for pathological examination. After the first session, the inside of the FNA needle was washed with saline for DNA extraction. KRAS mutations were examined using digital droplet PCR (dPCR). RESULTS The median needle puncture number used to obtain adequate pathological samples was two (range 1-6). In ten patients pathologically diagnosed with malignant pancreatic cancer, nine patients tested positive for a KRAS mutation. All patients who were not diagnosed with a malignant pancreatic cancer tested negative for a KRAS mutation. About half of surgically resected primary cancers (9/19) showed double KRAS mutations (G12V and G12D); however, all but one wash sample showed a single KRAS mutation, G12D. After including one patient who showed a malignant recurrence during follow-up, the sensitivities of a pathological diagnosis and KRAS analysis to detect recurrence were 90.9% and 81.8%, respectively. CONCLUSIONS KRAS mutation analysis of needle wash samples using dPCR is a new methodology for the diagnosis of the local recurrence of pancreatic cancer. The diagnostic ability of dPCR with a one-time needle wash sample was comparable to a pathological diagnosis with multiple samplings.
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Affiliation(s)
- Kazuyuki Matsumoto
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Hironari Kato
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Kazuhiro Nouso
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan.
| | - Soichiro Ako
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Hideaki Kinugasa
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Shigeru Horiguchi
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Yosuke Saragai
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Saimon Takada
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Shuntaro Yabe
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Shinichiro Muro
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Daisuke Uchida
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Takeshi Tomoda
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
| | - Hiroyuki Okada
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, 2-5-1 Shikata-cho, Okayama, 700-8558, Japan
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7
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Yu P, Dai Y, Dong J, Zhang L, Ping Y, Wang X, Wang D, Tao Z. ARMS TaqMan real-time PCR for genotyping factor V Leiden mutation in Han Chinese. Electrophoresis 2020; 41:2015-2020. [PMID: 32839994 DOI: 10.1002/elps.202000193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/05/2020] [Indexed: 11/07/2022]
Abstract
Factor V Leiden (FVLeiden ) is a missense mutation of 1691 position (G1691A) in exon 10 of FV gene, and being a genetic risk for venous thrombosis. Currently, there are several PCR-based methods for detecting FVLeiden mutation; however, these methods have disadvantages such as time-consuming, cumbersome steps and potentially hazardous gels. The aims of present study were to develop a simple, time-saving, accurate, and gel-free method, called amplification refractory mutation system (ARMS) TaqMan real-time PCR, for detecting FVLeiden mutation. We severally designed two specific reverse primers for mutant and wild-type through intentional introduction of mismatched nucleotide at the penultimate 3' position. Although target amplicon amplification efficiency is reduced, but another corresponding amplicon is almost completely inhibited. Then, specific TaqMan-probe was designed to detect target amplicon. Established method was used to detect 500 unselected samples in Han Chinese, the results showed 499 cases of wild-type and one heterozygote. Afterward, 50 randomly picked wild-type cases and one heterozygote were reexamined by bidirectional DNA sequencing, which is considered as "Gold standard method." Exhilaratingly, the results detected by the two methods were completely consistent. At last, allelic frequency of FVLeiden was calculated the in Han Chinese. Given the above results, A FVLeiden heterozygote has been found in 500 random samples in Han Chinese, and the allelic frequency was 0.1%. In conclusion, the ARMS TaqMan real-time PCR is an ideal detecting system for genotyping FVLeiden mutation in clinical application, and FVLeiden mutation exists in Han Chinese despite extremely low prevalence.
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Affiliation(s)
- Pan Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Yibei Dai
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Jiantao Dong
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Luyan Zhang
- Department of Laboratory Medicine, Ningbo Mingzhou Hospital, Ningbo, 315104, P. R. China
| | - Ying Ping
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Danhua Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
| | - Zhihua Tao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, P. R. China
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8
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Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer. Target Oncol 2020; 15:523-530. [PMID: 32770442 DOI: 10.1007/s11523-020-00743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. OBJECTIVE To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. PATIENTS AND METHODS Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. RESULTS The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an off-label therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. CONCLUSIONS The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.
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9
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Al Hashmi M, Sastry KS, Silcock L, Chouchane L, Mattei V, James N, Mathew R, Bedognetti D, De Giorgi V, Murtas D, Liu W, Chouchane A, Temanni R, Seliger B, Wang E, Marincola FM, Tomei S. Differential responsiveness to BRAF inhibitors of melanoma cell lines BRAF V600E-mutated. J Transl Med 2020; 18:192. [PMID: 32393282 PMCID: PMC7216681 DOI: 10.1186/s12967-020-02350-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background Most mutations in melanoma affect one critical amino acid on BRAF gene, resulting in the V600E substitution. Patient management is often based on the use of specific inhibitors targeting this mutation. Methods DNA and RNA mutation status was assessed in 15 melanoma cell lines by Sanger sequencing and RNA-seq. We tested the cell lines responsiveness to BRAF inhibitors (vemurafenib and PLX4720, BRAF-specific and sorafenib, BRAF non-specific). Cell proliferation was assessed by MTT colorimetric assay. BRAF V600E RNA expression was assessed by qPCR. Expression level of phosphorylated-ERK protein was assessed by Western Blotting as marker of BRAF activation. Results Three cell lines were discordant in the mutation detection (BRAF V600E at DNA level/Sanger sequencing and BRAF WT on RNA-seq). We initially postulated that those cell lines may express only the WT allele at the RNA level although mutated at the DNA level. A more careful analysis showed that they express low level of BRAF RNA and the expression may be in favor of the WT allele. We tested whether the discordant cell lines responded differently to BRAF-specific inhibitors. Their proliferation rate decreased after treatment with vemurafenib and PLX4720 but was not affected by sorafenib, suggesting a BRAF V600E biological behavior. Yet, responsiveness to the BRAF specific inhibitors was lower as compared to the control. Western Blot analysis revealed a decreased expression of p-ERK protein in the BRAF V600E control cell line and in the discordant cell lines upon treatment with BRAF-specific inhibitors. The discordant cell lines showed a lower responsiveness to BRAF inhibitors when compared to the BRAF V600E control cell line. The results obtained from the inhibition experiment and molecular analyses were also confirmed in three additional cell lines. Conclusion Cell lines carrying V600E mutation at the DNA level may respond differently to BRAF targeted treatment potentially due to a lower V600E RNA expression.
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Affiliation(s)
- Muna Al Hashmi
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Konduru S Sastry
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lee Silcock
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Valentina Mattei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Nicola James
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Rebecca Mathew
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Davide Bedognetti
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Valeria De Giorgi
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, USA
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Wei Liu
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Aouatef Chouchane
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Ramzi Temanni
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ena Wang
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Francesco M Marincola
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.,Refuge Biotechnologies, Menlo Park, CA, USA
| | - Sara Tomei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.
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10
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Igarashi T, Shimizu K, Usui K, Yokobori T, Ohtaki Y, Nakazawa S, Obayashi K, Yajima T, Nobusawa S, Ohkawa T, Katoh R, Motegi Y, Ogawa H, Harimoto N, Ichihara T, Mitani Y, Yokoo H, Mogi A, Shirabe K. Significance of RAS mutations in pulmonary metastases of patients with colorectal cancer. Int J Clin Oncol 2019; 25:641-650. [PMID: 31773354 DOI: 10.1007/s10147-019-01582-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND RAS/BRAF mutations of colorectal cancer (CRC) play a crucial role in carcinogenesis and cancer progression and need to be considered for the therapeutic strategy choice. We used next-generation-sequencing (NGS) technology to assess RAS/BRAF mutation differences between primary CRC and corresponding pulmonary metastases (PMs). METHODS We examined the mutation statuses of the KRAS 12/13/61/146, NRAS 12/13/61/146, and BRAF 600 codons in genomic DNA from fresh-frozen or formalin-fixed paraffin-embedded tissues derived from 34 primary lesions and 52 corresponding PMs from 36 patients with CRC. RESULTS We found RAS mutations in 76% (26/34) of primary CRC lesions and in 86% (31/36) of PMs. While 27% (7/26) of the primary CRC RAS mutations were heterogeneous, all the RAS mutations in PMs were homogeneous. Of the mutations in PMs, 71% (22/31) were KRAS G>A transitions, of which 82% (18/22) were KRAS G12D or G13D. The RAS mutation discordance between primary tumors and PMs was 12.1% (4/33). RAS mutations with the same genotyping were detected in all synchronous and metachronous PMs from 9 patients. We found no BRAF mutations in either primary or pulmonary tissues. CONCLUSION Our NGS analysis suggests that RAS mutations of PM of patients with CRC are more common than initially thought. The presence of KRAS mutations in CRC specimens, especially G12D or G13D mutations, seems to promote PM formation.
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Affiliation(s)
- Takamichi Igarashi
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kimihiro Shimizu
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
| | - Kengo Usui
- Genetic Diagnosis Technology Unit, RIKEN Center of Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takehiko Yokobori
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Department of Innovative Cancer Immunotherapy, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma, 371-8511, Japan
| | - Yoichi Ohtaki
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Seshiru Nakazawa
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kai Obayashi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Toshiki Yajima
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Department of Innovative Cancer Immunotherapy, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Sumihito Nobusawa
- Department of Human Pathology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Ohkawa
- Genetic Diagnosis Technology Unit, RIKEN Center of Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryuji Katoh
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Yoko Motegi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Hiroomi Ogawa
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Norifumi Harimoto
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Tatsuo Ichihara
- K.K. DNAFORM, 75-1 Ono-machi, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan
| | - Yasumasa Mitani
- K.K. DNAFORM, 75-1 Ono-machi, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan
| | - Hideaki Yokoo
- Department of Human Pathology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Akira Mogi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Ken Shirabe
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
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11
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Chen CL, Chen CK, Ho CL, Chi WM, Yeh CH, Hu SP, Friebe P, Palmer S, Huang CS. Clinical Evaluation of IntelliPlex™ KRAS G12/13 Mutation Kit for Detection of KRAS Mutations in Codon 12 and 13: A Novel Multiplex Approach. Mol Diagn Ther 2019; 23:645-656. [DOI: 10.1007/s40291-019-00418-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Jiang XW, Liu W, Zhu XY, Xu XX. Evaluation of EGFR mutations in NSCLC with highly sensitive droplet digital PCR assays. Mol Med Rep 2019; 20:593-603. [PMID: 31115577 PMCID: PMC6580028 DOI: 10.3892/mmr.2019.10259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/21/2019] [Indexed: 01/10/2023] Open
Abstract
Targeted drugs have been widely used in the treatment of patients with lung cancer, particularly for those with non-small cell lung cancer (NSCLC). Plasma cell-free DNA is an emerging clinical tool for the detection of epidermal growth factor receptor (EGFR) gene mutation in patients with lung cancer. Detection of circulating tumor (ct) DNA by droplet digital PCR (ddPCR) is a highly sensitive and minimally invasive alternative for the assessment and management of cancer. In the present study, four ddPCR systems were developed to detect the 19DELs, L858R, T790M and C797S mutations of the EGFR gene in plasma ctDNA samples, and all exhibited higher sensitivity compared with the amplification refractory mutation system (ARMS)-PCR assays. The results revealed that the sensitivity of the ddPCR assays for the four major types of EGFR mutant reached 0.04%. In total, 50 plasma ctDNA samples were collected from patients with NSCLC to detect the 19DELs, L858R, T790M and C797S mutations by ddPCR and ARMS-PCR. All the mutations except for C797S were detected and the concordance rates between ddPCR and ARMS-PCR were 96% (19DELs), 98% (L858R) and 100% (T790M). The fraction of EGFR mutation ranged from 0.43 to 68.07% using the ddPCR method. Therefore, the present study suggests that the four ddPCR testing systems could be used for early detection of EGFR mutations in plasma samples, so that patients can better select the targeted drugs according to the EGFR mutation.
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Affiliation(s)
- Xi-Wen Jiang
- Da An Gene Co., Ltd. of Sun Yat‑sen University, Guangzhou, Guangdong 510665, P.R. China
| | - Wei Liu
- Lu He Hospital Capital Medical University Beijing China, Beijing 100069, P.R. China
| | - Xiao-Ya Zhu
- Da An Gene Co., Ltd. of Sun Yat‑sen University, Guangzhou, Guangdong 510665, P.R. China
| | - Xiao-Xie Xu
- Da An Gene Co., Ltd. of Sun Yat‑sen University, Guangzhou, Guangdong 510665, P.R. China
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13
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Droplet digital PCR revealed high concordance between primary tumors and lymph node metastases in multiplex screening of KRAS mutations in colorectal cancer. Clin Exp Med 2019; 19:219-224. [PMID: 30661213 DOI: 10.1007/s10238-019-00545-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
The proto-oncogene KRAS belongs among the most frequently mutated genes in all types of cancer and is also very important oncogene related to colorectal tumors. The detection of mutations in this gene in primary tumor is a predictive biomarker for the anti-EGFR therapy in metastatic CRC (mCRC); however, the patients with wild-type KRAS can also show resistance to the personalized medicine. The droplet-based digital PCR technology has improved the analytical sensitivity of the mutations detection, which led us to the idea about the optimization of this approach for KRAS testing. In this study, we report the application of ddPCR technology in order to analyze the presence of KRAS mutations in primary tumor and matched metastasis in lymph nodes (LNs) from patients with mCRC and address the question, whether the improvement in the detection method can lower the discrepancies of KRAS mutations detection between the primary tumor and regional LNs. Genomic DNA with wtKRAS and commercial DNA with mtKRAS (G12D) were used to set up the ddPCR reaction. Formalin-fixed paraffin-embedded tissues from primary tumor and positive lymph node from 31 patients with mCRC were analyzed using ddPCR and Sanger sequencing. KRAS status of primary tumors was known; however, the mutation status of lymph nodes was not detected previously. From 31 samples of primary tumors, our results corresponded to results from IVD kit in 30 cases. For one patient, ddPCR detected KRAS mutation in comparison with negative result of the IVD kit. In the samples of metastatic infiltrated LNs, ddPCR detected 16 samples as a WT KRAS and 15 lymph nodes showed positivity for KRAS mutation, whereby Sanger sequencing found KRAS mutations in 8 cases only. We also found two cases where genetic conditions of KRAS gene differed between primary tumor and infiltrated lymph node, both "low-grade" adenocarcinoma. Our study approved that ddPCR method is adequate technique with high sensitivity and in the future may be used as a diagnostic tool for evaluation of KRAS mutations, especially in infiltrated LNs of patients with mCRC.
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14
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Prospective multicenter real-world RAS mutation comparison between OncoBEAM-based liquid biopsy and tissue analysis in metastatic colorectal cancer. Br J Cancer 2018; 119:1464-1470. [PMID: 30467411 PMCID: PMC6288144 DOI: 10.1038/s41416-018-0293-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background Liquid biopsy offers a minimally invasive alternative to tissue-based evaluation of mutational status in cancer. The goal of the present study was to evaluate the aggregate performance of OncoBEAM RAS mutation analysis in plasma of colorectal cancer (CRC) patients at 10 hospital laboratories in Spain where this technology is routinely implemented. Methods Circulating cell-free DNA from plasma was examined for RAS mutations using the OncoBEAM platform at each hospital laboratory. Results were then compared to those obtained from DNA extracted from tumour tissue from the same patient. Results The overall percentage agreement between plasma-based and tissue-based RAS mutation testing of the 236 participants was 89% (210/236; kappa, 0.770 (95% CI: 0.689–0.852)). Re-analysis of tissue from all discordant cases by BEAMing revealed two false negative and five false positive tumour tissue RAS results, with a final concordance of 92%. Plasma false negative results were found more frequently in patients with exclusive lung metastatic disease. Conclusions In this first prospective real-world RAS mutation performance comparison study, a high overall agreement was observed between results obtained from plasma and tissue samples. Overall, these findings indicate that the plasma-based BEAMing assay is a viable solution for rapid delivery of RAS mutation status to determine mCRC patient eligibility for anti-EGFR therapy.
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15
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Kim YJ, Chambers AG, Cecchi F, Hembrough T. Targeted data-independent acquisition for mass spectrometric detection of RAS mutations in formalin-fixed, paraffin-embedded tumor biopsies. J Proteomics 2018; 189:91-96. [DOI: 10.1016/j.jprot.2018.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/13/2018] [Accepted: 04/14/2018] [Indexed: 01/14/2023]
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16
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Kwon JH, Jeong BK, Yoon YS, Yu CS, Kim J. Utility of BRAF VE1 Immunohistochemistry as a Screening Tool for Colorectal Cancer Harboring BRAF V600E Mutation. J Pathol Transl Med 2018; 52:157-163. [PMID: 29590746 PMCID: PMC5964290 DOI: 10.4132/jptm.2018.03.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Background BRAF mutation has been recognized as an important biomarker of colorectal cancer (CRC) for targeted therapy and prognosis prediction. However, sequencing for every CRC case is not cost-effective. An antibody specific for BRAF V600E mutant protein has been introduced, and we thus examined the utility of BRAF VE1 immunohistochemistry for evaluating BRAF mutations in CRC. Methods Fifty-one BRAF-mutated CRCs and 100 age and sexmatched BRAF wild-type CRCs between 2005 and 2015 were selected from the archives of Asan Medical Center. Tissue microarrays were constructed and stained with BRAF VE1 antibody. Results Forty-nine of the 51 BRAF-mutant CRCs (96.1%) showed more than moderate cytoplasmic staining, except for two weakly stained cases. Six of 100 BRAF wild-type cases also stained positive with BRAF VE1 antibody; four stained weakly and two stained moderately. Normal colonic crypts showed nonspecific weak staining, and a few CRC cases exhibited moderate nuclear reactivity (3 BRAF-mutant and 10 BRAF wild-type cases). BRAF-mutated CRC patients had higher pathologic stages and worse survival than BRAF wild-type patients. Conclusions BRAF VE1 immunohistochemistry showed high sensitivity and specificity, but occasional nonspecific staining in tumor cell nuclei and normal colonic crypts may limit their routine clinical use. Thus, BRAF VE1 immunohistochemistry may be a useful screening tool for BRAF V600E mutation in CRCs, provided that additional sequencing studies can be done to confirm the mutation in BRAF VE1 antibody-positive cases.
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Affiliation(s)
- Jeong-Hwa Kwon
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byung-Kwan Jeong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Sik Yoon
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang Sik Yu
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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17
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McEvoy AC, Wood BA, Ardakani NM, Pereira MR, Pearce R, Cowell L, Robinson C, Grieu-Iacopetta F, Spicer AJ, Amanuel B, Ziman M, Gray ES. Droplet Digital PCR for Mutation Detection in Formalin-Fixed, Paraffin-Embedded Melanoma Tissues. J Mol Diagn 2018; 20:240-252. [DOI: 10.1016/j.jmoldx.2017.11.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022] Open
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18
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Gray PN, Vuong H, Tsai P, Lu HM, Mu W, Hsuan V, Hoo J, Shah S, Uyeda L, Fox S, Patel H, Janicek M, Brown S, Dobrea L, Wagman L, Plimack E, Mehra R, Golemis EA, Bilusic M, Zibelman M, Elliott A. TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy. Oncotarget 2018; 7:68206-68228. [PMID: 27626691 PMCID: PMC5356550 DOI: 10.18632/oncotarget.11910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/26/2016] [Indexed: 01/08/2023] Open
Abstract
The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.
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Affiliation(s)
| | - Huy Vuong
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Pei Tsai
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Wenbo Mu
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Jayne Hoo
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Swati Shah
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Lisa Uyeda
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | | | | | | | | | | | | | - Ranee Mehra
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
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19
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Grasselli J, Elez E, Caratù G, Matito J, Santos C, Macarulla T, Vidal J, Garcia M, Viéitez JM, Paéz D, Falcó E, Lopez Lopez C, Aranda E, Jones F, Sikri V, Nuciforo P, Fasani R, Tabernero J, Montagut C, Azuara D, Dienstmann R, Salazar R, Vivancos A. Concordance of blood- and tumor-based detection of RAS mutations to guide anti-EGFR therapy in metastatic colorectal cancer. Ann Oncol 2018; 28:1294-1301. [PMID: 28368441 PMCID: PMC5834108 DOI: 10.1093/annonc/mdx112] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Circulating tumor DNA (ctDNA) is a potential source for tumor genome analysis. We explored the concordance between the mutational status of RAS in tumor tissue and ctDNA in metastatic colorectal cancer (mCRC) patients to establish eligibility for anti-epidermal growth factor receptor (EGFR) therapy. Patients and methods A prospective-retrospective cohort study was carried out. Tumor tissue from 146 mCRC patients was tested for RAS status with standard of care (SoC) PCR techniques, and Digital PCR (BEAMing) was used both in plasma and tumor tissue. Results ctDNA BEAMing RAS testing showed 89.7% agreement with SoC (Kappa index 0.80; 95% CI 0.71 − 0.90) and BEAMing in tissue showed 90.9% agreement with SoC (Kappa index 0.83; 95% CI 0.74 − 0.92). Fifteen cases (10.3%) showed discordant tissue-plasma results. ctDNA analysis identified nine cases of low frequency RAS mutations that were not detected in tissue, possibly due to technical sensitivity or heterogeneity. In six cases, RAS mutations were not detected in plasma, potentially explained by low tumor burden or ctDNA shedding. Prediction of treatment benefit in patients receiving anti-EGFR plus irinotecan in second- or third-line was equivalent if tested with SoC PCR and ctDNA. Forty-eight percent of the patients showed mutant allele fractions in plasma below 1%. Conclusions Plasma RAS determination showed high overall agreement and captured a mCRC population responsive to anti-EGFR therapy with the same predictive level as SoC tissue testing. The feasibility and practicality of ctDNA analysis may translate into an alternative tool for anti-EGFR treatment selection.
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Affiliation(s)
- J Grasselli
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona.,Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Barcelona
| | - E Elez
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona.,Department of Medical Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona
| | - G Caratù
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona
| | - J Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona
| | - C Santos
- Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Barcelona
| | - T Macarulla
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona.,Department of Medical Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona
| | - J Vidal
- Department of Medical Oncology, Del Mar University Hospital, Barcelona
| | - M Garcia
- Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Barcelona
| | - J M Viéitez
- Department of Medical Oncology, Asturias University Hospital, Oviedo
| | - D Paéz
- Department of Medical Oncology, Santa Creu i Sant Pau University Hospital, Barcelona
| | - E Falcó
- Department of Medical Oncology, Son Llatzer University Hospital, Palma de Mallorca
| | - C Lopez Lopez
- Department of Medical Oncology, Marques de Valdecilla University Hospital, Santander
| | - E Aranda
- Department of Medical Oncology, Reina Sofía University Hospital, Córdoba, Spain
| | - F Jones
- Sysmex Inostics, Mundelein, USA
| | - V Sikri
- Sysmex Inostics, Mundelein, USA
| | - P Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona
| | - R Fasani
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona
| | - J Tabernero
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona.,Department of Medical Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona
| | - C Montagut
- Department of Medical Oncology, Del Mar University Hospital, Barcelona
| | - D Azuara
- Traslational Research Laboratory, Catalan Institute of Oncology, L'Hospitalet, Barcelona
| | - R Dienstmann
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona.,Oncology Data Science Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - R Salazar
- Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Barcelona
| | - A Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona
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20
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Vidal J, Muinelo L, Dalmases A, Jones F, Edelstein D, Iglesias M, Orrillo M, Abalo A, Rodríguez C, Brozos E, Vidal Y, Candamio S, Vázquez F, Ruiz J, Guix M, Visa L, Sikri V, Albanell J, Bellosillo B, López R, Montagut C. Plasma ctDNA RAS mutation analysis for the diagnosis and treatment monitoring of metastatic colorectal cancer patients. Ann Oncol 2018; 28:1325-1332. [PMID: 28419195 PMCID: PMC5834035 DOI: 10.1093/annonc/mdx125] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background RAS assessment is mandatory for therapy decision in metastatic colorectal cancer (mCRC) patients. This determination is based on tumor tissue, however, genotyping of circulating tumor (ct)DNA offers clear advantages as a minimally invasive method that represents tumor heterogeneity. Our study aims to evaluate the use of ctDNA as an alternative for determining baseline RAS status and subsequent monitoring of RAS mutations during therapy as a component of routine clinical practice. Patients and methods RAS mutational status in plasma was evaluated in mCRC patients by OncoBEAM™ RAS CRC assay. Concordance of results in plasma and tissue was retrospectively evaluated. RAS mutations were also prospectively monitored in longitudinal plasma samples from selected patients. Results Analysis of RAS in tissue and plasma samples from 115 mCRC patients showed a 93% overall agreement. Plasma/tissue RAS discrepancies were mainly explained by spatial and temporal tumor heterogeneity. Analysis of clinico-pathological features showed that the site of metastasis (i.e. peritoneal, lung), the histology of the tumor (i.e. mucinous) and administration of treatment previous to blood collection negatively impacted the detection of RAS in ctDNA. In patients with baseline mutant RAS tumors treated with chemotherapy/antiangiogenic, longitudinal analysis of RAS ctDNA mirrored response to treatment, being an early predictor of response. In patients RAS wt, longitudinal monitoring of RAS ctDNA revealed that OncoBEAM was useful to detect emergence of RAS mutations during anti-EGFR treatment. Conclusion The high overall agreement in RAS mutational assessment between plasma and tissue supports blood-based testing with OncoBEAM™ as a viable alternative for genotyping RAS of mCRC patients in routine clinical practice. Our study describes practical clinico-pathological specifications to optimize RAS ctDNA determination. Moreover, OncoBEAM™ is useful to monitor RAS in patients undergoing systemic therapy to detect resistance and evaluate the efficacy of particular treatments.
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Affiliation(s)
- J Vidal
- Cancer Research Program, FIMIM Hospital del Mar, Barcelona, Spain.,Medical Oncology Department, Hospital del Mar, Barcelona
| | - L Muinelo
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - A Dalmases
- Pathology Department, Hospital del Mar, Barcelona
| | - F Jones
- Sysmex Inostics Inc., Mundelein, USA
| | | | - M Iglesias
- Cancer Research Program, FIMIM Hospital del Mar, Barcelona, Spain.,Pathology Department, Hospital del Mar, Barcelona
| | - M Orrillo
- Medical Oncology Department, Hospital del Mar, Barcelona
| | - A Abalo
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - C Rodríguez
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - E Brozos
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - Y Vidal
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - S Candamio
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - F Vázquez
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - J Ruiz
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - M Guix
- Medical Oncology Department, Hospital del Mar, Barcelona
| | - L Visa
- Medical Oncology Department, Hospital del Mar, Barcelona
| | - V Sikri
- Sysmex Inostics Inc., Mundelein, USA
| | - J Albanell
- Cancer Research Program, FIMIM Hospital del Mar, Barcelona, Spain.,Medical Oncology Department, Hospital del Mar, Barcelona.,Universitat Pompeu Fabra, Barcelona, Spain
| | - B Bellosillo
- Medical Oncology Department, Hospital del Mar, Barcelona.,Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - R López
- Traslational Medical Oncology Group (Oncomet)/Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) CIBERONC, Santiago de Compostela
| | - C Montagut
- Cancer Research Program, FIMIM Hospital del Mar, Barcelona, Spain.,Medical Oncology Department, Hospital del Mar, Barcelona
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21
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McEvoy AC, Calapre L, Pereira MR, Giardina T, Robinson C, Khattak MA, Meniawy TM, Pritchard AL, Hayward NK, Amanuel B, Millward M, Ziman M, Gray ES. Sensitive droplet digital PCR method for detection of TERT promoter mutations in cell free DNA from patients with metastatic melanoma. Oncotarget 2017; 8:78890-78900. [PMID: 29108273 PMCID: PMC5668006 DOI: 10.18632/oncotarget.20354] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/25/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Currently mainly BRAF mutant circulating tumor DNA (ctDNA) is utilized to monitor patients with melanoma. TERT promoter mutations are common in various cancers and found in up to 70% of melanomas, including half of BRAF wild-type cases. Therefore, a sensitive method for detection of TERT promoter mutations would increase the number of patients that could be monitored through ctDNA analysis. METHODS A droplet digital PCR (ddPCR) assay was designed for the concurrent detection of chr5:1,295,228 C>T and chr5:1,295,250 C>T TERT promoter mutations. The assay was validated using 39 melanoma cell lines and 22 matched plasma and tumor samples. In addition, plasma samples from 56 metastatic melanoma patients and 56 healthy controls were tested for TERT promoter mutations. RESULTS The established ddPCR assay detected TERT promoter mutations with a lower limit of detection (LOD) of 0.17%. Total concordance was demonstrated between ddPCR and Sanger sequencing in all cell lines except one, which carried a second mutation within the probe binding-site. Concordance between matched plasma and tumor tissue was 68% (15/22), with a sensitivity of 53% (95% CI, 27%-79%) and a specificity of 100% (95% CI, 59%-100%). A significantly longer PFS (p=0.028) was evident in ctDNA negative patients. Importantly, our TERT promoter mutations ddPCR assay allowed detection of ctDNA in 11 BRAF wild-type cases. CONCLUSIONS The TERT promoter mutation ddPCR assay offers a sensitive test for molecular analysis of melanoma tumors and ctDNA, with the potential to be applied to other cancers.
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Affiliation(s)
- Ashleigh C. McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Michelle R. Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tindaro Giardina
- Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Cleo Robinson
- Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Muhammad A. Khattak
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Tarek M. Meniawy
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | | | - Nicholas K. Hayward
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Benhur Amanuel
- Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Michael Millward
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
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22
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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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23
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Wu LR, Chen SX, Wu Y, Patel AA, Zhang DY. Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nat Biomed Eng 2017; 1:714-723. [PMID: 29805844 DOI: 10.1038/s41551-017-0126-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rare DNA-sequence variants hold important clinical and biological information, but existing detection techniques are expensive, complex, allele-specific, or don't allow for significant multiplexing. Here, we report a temperature-robust polymerase-chain-reaction method, which we term blocker displacement amplification (BDA), that selectively amplifies all sequence variants, including single-nucleotide variants (SNVs), within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences. This allows for easy detection and quantitation of hundreds of potential variants originally at ≤0.1% in allele frequency. BDA is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 °C to 64 °C. To show the sequence generality of BDA, we demonstrate enrichment of 156 SNVs and the reliable detection of single-digit copies. We also show that the BDA detection of rare driver mutations in cell-free DNA samples extracted from the blood plasma of lung-cancer patients is highly consistent with deep sequencing using molecular lineage tags, with a receiver operator characteristic accuracy of 95%.
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Affiliation(s)
- Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Sherry X Chen
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Yalei Wu
- Thermo Fisher, San Francisco, CA, 94080, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
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24
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Sharma A, Zhang G, Aslam S, Yu K, Chee M, Palma JF. Novel Approach for Clinical Validation of the cobas KRAS Mutation Test in Advanced Colorectal Cancer. Mol Diagn Ther 2017; 20:231-40. [PMID: 26984642 PMCID: PMC4879158 DOI: 10.1007/s40291-016-0193-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim Our objective was to assess the performance of the cobas test versus comparators for KRAS mutation status and predicting clinical response to anti-epidermal growth factor receptor (EGFR) therapy in patients with metastatic colorectal cancer (mCRC). Methods mCRC samples from 398 patients from Roche study NO16968 (XELOXA) and 82 supplemental samples were tested with the cobas® KRAS mutation test (cobas test), the therascreen® KRAS RGQ PCR kit test (therascreen test), and Sanger sequencing as the reference method for detecting mutations in codons 12/13. Results For 461 eligible samples, the cobas test, therascreen test, and sequencing had invalid results for 5.2, 10.8, and 2.6 % of specimens, respectively. Valid cobas and therascreen test results had similar KRAS mutation-positive rates (37.3 vs. 36.3 %, respectively); sequencing was 28.5 %. Positive and negative percent agreement (PPA/NPA) between the cobas test and sequencing was 96.9 % (95 % confidence interval [CI] 92.2–98.8), and 88.7 % (95 % CI 84.7–91.8), respectively. PPA/NPA between the cobas and therascreen tests was 93.3 % (95 % CI 88.1–96.3) and 96.5 % (95 % CI 93.5–98.1), respectively. Bridging analysis from NCIC-CO.17 and NCT00113763 using the cobas test yielded modeled hazard ratios for overall survival and progression-free survival (PFS) of 0.558 (95 % CI 0.422–0.752) and 0.413 (95 % CI 0.304–0.550), respectively, for cetuximab and 0.989 (95 % CI 0.778–1.299) and 0.471 (95 % CI 0.360–0.626), respectively, for panitumumab, demonstrating significant efficacy in the KRAS-negative population for PFS. Conclusion The cobas test showed similar accuracy to the therascreen test for detecting KRAS mutations and could appropriately identify mCRC patients ineligible for anti-EGFR therapy as demonstrated by bridging analysis results. Electronic supplementary material The online version of this article (doi:10.1007/s40291-016-0193-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abha Sharma
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Guili Zhang
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Shagufta Aslam
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Karen Yu
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Melody Chee
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - John F Palma
- Medical Affairs Department, Roche Molecular Systems, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA.
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25
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Lee HS, Kim WH, Kwak Y, Koh J, Bae JM, Kim KM, Chang MS, Han HS, Kim JM, Kim HW, Chang HK, Choi YH, Park JY, Gu MJ, Lhee MJ, Kim JY, Kim HS, Cho MY. Molecular Testing for Gastrointestinal Cancer. J Pathol Transl Med 2017; 51:103-121. [PMID: 28219002 PMCID: PMC5357760 DOI: 10.4132/jptm.2017.01.24] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 12/20/2022] Open
Abstract
With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2-4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus-positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians.
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Affiliation(s)
- Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mee Soo Chang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Hye Seung Han
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Joon Mee Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Hwal Woong Kim
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
| | - Hee Kyung Chang
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Young Hee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
| | - Ji Y. Park
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Mi Jin Gu
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
| | - Min Jin Lhee
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
| | - Jung Yeon Kim
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mee-Yon Cho
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Gastrointestinal Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
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26
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Abstract
Monoclonal antibodies (mAbs) and fusion proteins with an Fc portion of immunoglobulin G (IgG) are emblematic of the remarkable expansion of biopharmaceuticals. Despite their biological origin, these products display an interindividual variability in their efficacy and/or side effects, which must be taken into consideration. Biological monitoring allowing for adapted prescription and dose adjustments may lead to therapeutic optimization and limitation of the high costs of these drugs. Herein, we review the biological theranostic of mAbs and Fc fusion proteins, including pre-treatment analyses, monitoring of efficacy, therapeutic drug monitoring, and monitoring of side effects. Supported by concrete evidence, a specific interest is given to individualised therapeutic monitoring that combines intention to treat, biomarkers of efficacy and adaptation of serum concentrations.
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Affiliation(s)
- Benjamin Chaigne
- Université Paris Descartes, Faculté de Médecine, Service de Médecine Interne, Centre de Référence Pour les Vascularites Nécrosantes et la Sclérodermie Systémique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France
| | - Hervé Watier
- CHRU de Tours, Laboratoire d'Immunologie, France; Université François-Rabelais de Tours, France; CNRS, UMR 7292, Tours, France.
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27
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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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28
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Botezatu IV, Panchuk IO, Stroganova AM, Senderovich AI, Kondratova VN, Shelepov VP, Lichtenstein AV. Scanning for KRAS, NRAS, BRAF, and PIK3CA mutations by DNA melting analysis with TaqMan probes. Mol Biol 2017. [DOI: 10.1134/s002689331701006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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29
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Sho S, Court CM, Kim S, Braxton DR, Hou S, Muthusamy VR, Watson RR, Sedarat A, Tseng HR, Tomlinson JS. Digital PCR Improves Mutation Analysis in Pancreas Fine Needle Aspiration Biopsy Specimens. PLoS One 2017; 12:e0170897. [PMID: 28125707 PMCID: PMC5268428 DOI: 10.1371/journal.pone.0170897] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
Applications of precision oncology strategies rely on accurate tumor genotyping from clinically available specimens. Fine needle aspirations (FNA) are frequently obtained in cancer management and often represent the only source of tumor tissues for patients with metastatic or locally advanced diseases. However, FNAs obtained from pancreas ductal adenocarcinoma (PDAC) are often limited in cellularity and/or tumor cell purity, precluding accurate tumor genotyping in many cases. Digital PCR (dPCR) is a technology with exceptional sensitivity and low DNA template requirement, characteristics that are necessary for analyzing PDAC FNA samples. In the current study, we sought to evaluate dPCR as a mutation analysis tool for pancreas FNA specimens. To this end, we analyzed alterations in the KRAS gene in pancreas FNAs using dPCR. The sensitivity of dPCR mutation analysis was first determined using serial dilution cell spiking studies. Single-cell laser-microdissection (LMD) was then utilized to identify the minimal number of tumor cells needed for mutation detection. Lastly, dPCR mutation analysis was performed on 44 pancreas FNAs (34 formalin-fixed paraffin-embedded (FFPE) and 10 fresh (non-fixed)), including samples highly limited in cellularity (100 cells) and tumor cell purity (1%). We found dPCR to detect mutations with allele frequencies as low as 0.17%. Additionally, a single tumor cell could be detected within an abundance of normal cells. Using clinical FNA samples, dPCR mutation analysis was successful in all preoperative FNA biopsies tested, and its accuracy was confirmed via comparison with resected tumor specimens. Moreover, dPCR revealed additional KRAS mutations representing minor subclones within a tumor that were not detected by the current clinical gold standard method of Sanger sequencing. In conclusion, dPCR performs sensitive and accurate mutation analysis in pancreas FNAs, detecting not only the dominant mutation subtype, but also the additional rare mutation subtypes representing tumor heterogeneity.
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Affiliation(s)
- Shonan Sho
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- * E-mail:
| | - Colin M. Court
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephen Kim
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - David R. Braxton
- Department of Pathology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - V. Raman Muthusamy
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Rabindra R. Watson
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Alireza Sedarat
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Digestive Diseases, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, United States of America
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - James S. Tomlinson
- Department of Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Surgery, Greater Los Angeles Veteran’s Affairs Administration, Los Angeles, California, United States of America
- UCLA Center for Pancreatic Diseases, University of California Los Angeles, Los Angeles, California, United States of America
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30
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Lee SH, Chung AM, Lee A, Oh WJ, Choi YJ, Lee YS, Jung ES. KRAS Mutation Test in Korean Patients with Colorectal Carcinomas: A Methodological Comparison between Sanger Sequencing and a Real-Time PCR-Based Assay. J Pathol Transl Med 2016; 51:24-31. [PMID: 28013534 PMCID: PMC5267542 DOI: 10.4132/jptm.2016.10.03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 10/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. Methods We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. Results KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. Conclusions The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
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Affiliation(s)
- Sung Hak Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Arthur Minwoo Chung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo Jin Oh
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeong Jin Choi
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn-Soo Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun Sun Jung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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Orue A, Rieber M. Optimized Multiplex Detection of 7 KRAS Mutations by Taqman Allele-Specific qPCR. PLoS One 2016; 11:e0163070. [PMID: 27632281 PMCID: PMC5025196 DOI: 10.1371/journal.pone.0163070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Establishing the KRAS mutational status of tumor samples is essential to manage patients with colorectal or lung cancer, since these mutations preclude treatment with monoclonal anti-epidermal growth factor receptor (EGFR) antibodies. We report an inexpensive, rapid multiplex allele-specific qPCR method detecting the 7 most clinically relevant KRAS somatic mutations with concomitant amplification of non-mutated KRAS in tumor cells and tissues from CRC patients. Positive samples evidenced in the multiplex assay were further subjected to individual allele-specific analysis, to define the specific mutation. Reference human cancer DNA harbouring either G12A, G12C, G12D, G12R, G12S, G12V and G13D confirmed assay specificity with ≤1% sensitivity of mutant alleles. KRAS multiplex mutation analysis usefulness was also demonstrated with formalin-fixed paraffin embedded (FFPE) from CRC biopsies. CONCLUSION Co-amplification of non-mutated DNA avoided false negatives from degraded samples. Moreover, this cost effective assay is compatible with mutation detection by DNA sequencing in FFPE tissues, but with a greater sensitivity when mutant DNA concentrations are limiting.
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Affiliation(s)
- Andrea Orue
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
| | - Manuel Rieber
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
- * E-mail:
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Han KH, Kim AR, Kim MY, Ahn S, Oh SH, Song JH, Choi BY. Establishment of a Flexible Real-Time Polymerase Chain Reaction-Based Platform for Detecting Prevalent Deafness Mutations Associated with Variable Degree of Sensorineural Hearing Loss in Koreans. PLoS One 2016; 11:e0161756. [PMID: 27583405 PMCID: PMC5008798 DOI: 10.1371/journal.pone.0161756] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
Many cutting-edge technologies based on next-generation sequencing (NGS) have been employed to identify candidate variants responsible for sensorineural hearing loss (SNHL). However, these methods have limitations preventing their wide clinical use for primary screening, in that they remain costly and it is not always suitable to analyze massive amounts of data. Several different DNA chips have been developed for screening prevalent mutations at a lower cost. However, most of these platforms do not offer the flexibility to add or remove target mutations, thereby limiting their wider use in a field that requires frequent updates. Therefore, we aimed to establish a simpler and more flexible molecular diagnostic platform based on ethnicity-specific mutation spectrums of SNHL, which would enable bypassing unnecessary filtering steps in a substantial portion of cases. In addition, we expanded the screening platform to cover varying degrees of SNHL. With this aim, we selected 11 variants of 5 genes (GJB2, SLC26A4, MTRNR1, TMPRSS3, and CDH23) showing high prevalence with varying degrees in Koreans and developed the U-TOP™ HL Genotyping Kit, a real-time PCR-based method using the MeltingArray technique and peptide nucleic acid probes. The results of 271 DNA samples with wild type sequences or mutations in homo- or heterozygote form were compared between the U-TOP™ HL Genotyping Kit and Sanger sequencing. The positive and negative predictive values were 100%, and this method showed perfect agreement with Sanger sequencing, with a Kappa value of 1.00. The U-TOP™ HL Genotyping Kit showed excellent performance in detecting varying degrees and phenotypes of SNHL mutations in both homozygote and heterozygote forms, which are highly prevalent in the Korean population. This platform will serve as a useful and cost-effective first-line screening tool for varying degrees of genetic SNHL and facilitate genome-based personalized hearing rehabilitation for the Korean population.
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Affiliation(s)
- Kyu-Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Soyeon Ahn
- Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ju Hun Song
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Korea
- * E-mail:
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Can Molecular Biomarkers Change the Paradigm of Pancreatic Cancer Prognosis? BIOMED RESEARCH INTERNATIONAL 2016; 2016:4873089. [PMID: 27689078 PMCID: PMC5023838 DOI: 10.1155/2016/4873089] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/28/2016] [Accepted: 08/03/2016] [Indexed: 12/20/2022]
Abstract
Pancreatic ductal adenocarcinoma is one of the most lethal types of tumour, and its incidence is rising worldwide. Although survival can be improved when these tumours are detected at an early stage, this cancer is usually asymptomatic, and the disease only becomes apparent after metastasis. The only prognostic biomarker approved by the FDA to date is carbohydrate antigen 19-9 (CA19-9); however, the specificity of this biomarker has been called into question, and diagnosis is usually based on clinical parameters. Tumour size, degree of differentiation, lymph node status, presence of distant metastasis at diagnosis, protein levels of KI-67 or C-reactive protein, and mutational status of P53, KRAS, or BRCA2 are the most useful biomarkers in clinical practice. In addition to these, recent translational research has provided evidence of new biomarkers based on different molecules involved in endoplasmic reticulum stress, epithelial-to-mesenchymal transition, and noncoding RNA panels, especially microRNAs and long noncoding RNAs. These new prospects open new paths to tumour detection using minimally or noninvasive techniques such as liquid biopsies. To find sensitive and specific biomarkers to manage these patients constitutes a challenge for the research community and for public health policies.
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Cree IA. Progress and potential of RAS mutation detection for diagnostics and companion diagnostics. Expert Rev Mol Diagn 2016; 16:1067-1072. [PMID: 27494709 DOI: 10.1080/14737159.2016.1221345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The importance of RAS mutation in carcinogenesis is established, and knowledge of an individual cancer's mutation status is important for optimal treatment. Areas covered: This paper is restricted to RAS testing in cancer, and highlights papers relevant to current practice. Expert commentary: Multiple laboratory methods are available for RAS gene analysis. PCR is commonly used to determine RAS status, providing a robust and inexpensive technology for clinical use. Next generation sequencing (NGS) platforms are changing the way in which mutation status is determined, though they require considerable expertise. Pre-analytical issues affect both methods and should be considered. The interpretation and reporting of results is not simple, particularly for NGS. External quality assurance is a pre-requisite for success, and is mandated by most laboratory accreditation schemes. The use of RAS testing is now extending beyond biopsy material to include the detection of mutations in circulating cell-free DNA and tumour cells.
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Affiliation(s)
- Ian A Cree
- a Department of Pathology , University Hospitals Coventry and Warwickshire , Coventry , United Kingdom
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36
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Mack E, Stabla K, Riera-Knorrenschild J, Moll R, Neubauer A, Brendel C. A rational two-step approach to KRAS mutation testing in colorectal cancer using high resolution melting analysis and pyrosequencing. BMC Cancer 2016; 16:585. [PMID: 27485514 PMCID: PMC4971616 DOI: 10.1186/s12885-016-2589-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 01/03/2023] Open
Abstract
Background KRAS mutation testing is mandatory in the management of metastatic colorectal cancer prior to treatment with anti-EGFR antibodies as patients whose tumors express mutant KRAS do not benefit from these agents. Although the U.S. Food and Drug Administration has recently approved two in-vitro diagnostics kits for determination of KRAS status, there is generally no consensus on the preferred method and new tests are continuously being developed. Most of these techniques focus on the hotspot mutations at codons 12 and 13 of the KRAS gene. Methods We describe a two-step approach to KRAS codon 12/13 mutation testing involving high resolution melting analysis (HRM) followed by pyrosequencing using the Therascreen KRAS Pyro kit (Qiagen) of only those samples that are not clearly identified as KRAS wildtype or mutant by HRM. First, we determined KRAS status in a panel of 61 colorectal cancer samples using both methods to compare technical performance and concordance of results. Subsequently, we evaluated practicability and costs of our concept in an independent set of 120 colorectal cancer samples in a routine diagnostic setting. Results HRM and pyrosequencing appeared to be equally sensitive, allowing for clear detection of mutant alleles at a mutant allele frequency ≥12.5 %. Pyrosequencing yielded more exploitable results due to lower input requirements and a lower rate of analysis failures. KRAS codon 12/13 status was called concordantly for 98.2 % (56/57) of all samples that could be successfully analysed by both methods and 100 % (19/19) of samples that were identified mutant by HRM. Reviewing the actual effort and expenses for KRAS mutation testing in our laboratory revealed, that the selective use of pyrosequencing for only those samples that could not be analysed by HRM increased the fraction of valid results from 87.5 % for HRM alone to 99.2 % (119/120) while allowing for a net reduction of operational costs of >75 % compared to pyrosequencing alone. Conclusions Combination of HRM and pyrosequencing in a two-step diagnostic procedure constitutes a reliable and economic analysis platform for KRAS mutation testing in colorectal cancer in a clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabeth Mack
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Kathleen Stabla
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Jorge Riera-Knorrenschild
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Roland Moll
- Institut für Pathologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Andreas Neubauer
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Cornelia Brendel
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany.
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Sloane HS, Landers JP, Kelly KA. Hybridization-Induced Aggregation Technology for Practical Clinical Testing: KRAS Mutation Detection in Lung and Colorectal Tumors. J Mol Diagn 2016; 18:546-53. [PMID: 27289420 DOI: 10.1016/j.jmoldx.2016.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/04/2016] [Accepted: 02/18/2016] [Indexed: 11/29/2022] Open
Abstract
KRAS mutations have emerged as powerful predictors of response to targeted therapies in the treatment of lung and colorectal cancers; thus, prospective KRAS genotyping is essential for appropriate treatment stratification. Conventional mutation testing technologies are not ideal for routine clinical screening, as they often involve complex, time-consuming processes and/or costly instrumentation. In response, we recently introduced a unique analytical strategy for revealing KRAS mutations, based on the allele-specific hybridization-induced aggregation (HIA) of oligonucleotide probe-conjugated microbeads. Using simple, inexpensive instrumentation, this approach allows for the detection of any common KRAS mutation in <10 minutes after PCR. Here, we evaluate the clinical utility of the HIA method for mutation detection (HIAMD). In the analysis of 20 lung and colon tumor pathology specimens, we observed a 100% correlation between the KRAS mutation statuses determined by HIAMD and sequencing. In addition, we were able to detect KRAS mutations in a background of 75% wild-type DNA-a finding consistent with that reported for sequencing. With this, we show that HIAMD allows for the rapid and cost-effective detection of KRAS mutations, without compromising analytical performance. These results indicate the validity of HIAMD as a mutation-testing technology suitable for practical clinical testing. Further expansion of this platform may involve the detection of mutations in other key oncogenic pathways.
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Affiliation(s)
- Hillary S Sloane
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia; Department of Pathology, University of Virginia, Charlottesville, Virginia; Department of Mechanical Engineering, University of Virginia, Charlottesville, Virginia
| | - Kimberly A Kelly
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia; Robert M. Berne Cardiovascular Research Center, School of Medicine, University of Virginia, Charlottesville, Virginia.
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Diagnostic RAS mutation analysis by polymerase chain reaction (PCR). BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 8:29-32. [PMID: 27335808 PMCID: PMC4906127 DOI: 10.1016/j.bdq.2016.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/26/2016] [Accepted: 05/17/2016] [Indexed: 02/07/2023]
Abstract
RAS mutation analysis is an important companion diagnostic test. Treatment of colorectal cancer with anti-Epidermal Growth Factor Receptor (EGFR) therapy requires demonstration of RAS mutation status (both KRAS and NRAS), and it is good practice to include BRAF. In Non-Small Cell Lung Cancer (NSCLC) and melanoma, assessment of RAS mutation status can be helpful in triaging patient samples for more extensive testing. This mini-review will discuss the role of PCR methods in providing rapid diagnostic information for cancer patients.
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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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Jo P, König A, Schirmer M, Kitz J, Conradi LC, Azizian A, Bernhardt M, Wolff HA, Grade M, Ghadimi M, Ströbel P, Schildhaus HU, Gaedcke J. Heterogeneity of KRAS Mutation Status in Rectal Cancer. PLoS One 2016; 11:e0153278. [PMID: 27064574 PMCID: PMC4827807 DOI: 10.1371/journal.pone.0153278] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 03/25/2016] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Anti-EGFR targeted therapy is of increasing importance in advanced colorectal cancer and prior KRAS mutation testing is mandatory for therapy. However, at which occasions this should be performed is still under debate. We aimed to assess in patients with locally advanced rectal cancer whether there is intra-specimen KRAS heterogeneity prior to and upon preoperative chemoradiotherapy (CRT), and if there are any changes in KRAS mutation status due to this intervention. MATERIALS AND METHODS KRAS mutation status analyses were performed in 199 tumor samples from 47 patients with rectal cancer. To evaluate the heterogeneity between different tumor areas within the same tumor prior to preoperative CRT, 114 biopsies from 34 patients (mean 3 biopsies per patient) were analyzed (pre-therapeutic intratumoral heterogeneity). For the assessment of heterogeneity after CRT residual tumor tissue (85 samples) from 12 patients (mean 4.2 tissue samples per patient) were analyzed (post-therapeutic intratumoral heterogeneity) and assessment of heterogeneity before and after CRT was evaluated in corresponding patient samples (interventional heterogeneity). Primer extension method (SNaPshot™) was used for initial KRAS mutation status testing for Codon 12, 13, 61, and 146. Discordant results by this method were reevaluated by using the FDA-approved KRAS Pyro Kit 24, V1 and the RAS Extension Pyro Kit 24, V1 Kit (therascreen® KRAS test). RESULTS For 20 (43%) out of the 47 patients, a KRAS mutation was detected. With 12 out of 20, the majority of these mutations affected codon 35. We did not obtained evidence that CRT results in changes of the KRAS mutation pattern. In addition, no intratumoral heterogeneity in the KRAS mutational status could be proven. This was true for both the biopsies prior to CRT and the resection specimens thereafter. The discrepancy observed in some samples when using the SNaPshot™ assay was due to insufficient sensitivity of this technique upon massive tumor regression by CRT as application of the therascreen® KRAS test revealed concordant results. CONCLUSION Our results indicate that the KRAS mutation status at the primary tumor site of rectal cancer is homogenous. Its assessment for therapeutic decisions is feasible in pre-therapeutic biopsies as well as in post-therapeutic resected specimens. The amount of viable tumor cells seems to be an important determinant for assay sensitivity and should thus be considered for selection of the analytical method.
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Affiliation(s)
- Peter Jo
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Alexander König
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Center Goettingen, Goettingen, Germany
| | - Markus Schirmer
- Department of Clinical Pharmacology, University Medical Center Goettingen, Goettingen, Germany
| | - Julia Kitz
- Department of Pathology, University Medical Center Goettingen, Goettingen, Germany
| | - Lena-Christin Conradi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Azadeh Azizian
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Markus Bernhardt
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | | | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Philipp Ströbel
- Department of Pathology, University Medical Center Goettingen, Goettingen, Germany
| | | | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany
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Luo D, Smith JA, Meadows NA, Schuh A, Manescu KE, Bure K, Davies B, Horne R, Kope M, DiGiusto DL, Brindley DA. A Quantitative Assessment of Factors Affecting the Technological Development and Adoption of Companion Diagnostics. Front Genet 2016; 6:357. [PMID: 26858745 PMCID: PMC4730156 DOI: 10.3389/fgene.2015.00357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022] Open
Abstract
Rapid innovation in (epi)genetics and biomarker sciences is driving a new drug development and product development pathway, with the personalized medicine era dominated by biologic therapeutics and companion diagnostics. Companion diagnostics (CDx) are tests and assays that detect biomarkers and specific mutations to elucidate disease pathways, stratify patient populations, and target drug therapies. CDx can substantially influence the development and regulatory approval for certain high-risk biologics. However, despite the increasingly important role of companion diagnostics in the realization of personalized medicine, in the USA, there are only 23 Food and Drug Administration (FDA) approved companion diagnostics on the market for 11 unique indications. Personalized medicines have great potential, yet their use is currently constrained. A major factor for this may lie in the increased complexity of the companion diagnostic and corresponding therapeutic development and adoption pathways. Understanding the market dynamics of companion diagnostic/therapeutic (CDx/Rx) pairs is important to further development and adoption of personalized medicine. Therefore, data collected on a variety of factors may highlight incentives or disincentives driving the development of companion diagnostics. Statistical analysis for 36 hypotheses resulted in two significant relationships and 34 non-significant relationships. The sensitivity of the companion diagnostic was the only factor that significantly correlated with the price of the companion diagnostic. This result indicates that while there is regulatory pressure for the diagnostic and pharmaceutical industry to collaborate and co-develop companion diagnostics for the approval of personalized therapeutics, there seems to be a lack of parallel economic collaboration to incentivize development of companion diagnostics.
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Affiliation(s)
- Dee Luo
- Department of Biological Basis of Behavior, University of Pennsylvania Phildephila, PA, USA
| | - James A Smith
- The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation, University of OxfordOxford, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of OxfordOxford, UK
| | | | - A Schuh
- National Institute of Health Research, Biomedical Research Centre, Molecular Diagnostic Centre, Oxford University Hospitals Oxford, UK
| | - Katie E Manescu
- Department of Biochemical Engineering, University College London London, UK
| | - Kim Bure
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Oxford, UK
| | | | - Rob Horne
- The UCL School of Pharmacy, University College London London, UK
| | - Mike Kope
- SENS Research Foundation Mountain View, CA, USA
| | - David L DiGiusto
- Stem Cell and Cellular Therapeutics Operations at Stanford University Hospital and Clinic Stanford, CA, USA
| | - David A Brindley
- Stem Cell and Cellular Therapeutics Operations at Stanford University Hospital and ClinicStanford, CA, USA; The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation, University of OxfordOxford, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of OxfordOxford, UK; USCF-Stanford Center of Excellence in Regulatory Science and InnovationSan Francisco, CA, USA; Centre for Behavioural Medicine, UCL School of Pharmacy, University College LondonLondon, UK; Harvard Stem Cell InstituteCambridge, MA, USA
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Gao J, Wu H, Wang L, Zhang H, Duan H, Lu J, Liang Z. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR. BMJ Open 2016; 6:e009532. [PMID: 26747035 PMCID: PMC4716245 DOI: 10.1136/bmjopen-2015-009532] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. SETTING Beijing, China. PARTICIPANTS 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. METHODS RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. RESULTS 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. CONCLUSIONS The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes.
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Affiliation(s)
- Jie Gao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Li Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
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Botezatu IV, Nechaeva IO, Stroganova АМ, Senderovich AI, Kondratova VN, Shelepov VP, Lichtenstein AV. Optimization of melting analysis with TaqMan probes for detection of KRAS, NRAS, and BRAF mutations. Anal Biochem 2015; 491:75-83. [DOI: 10.1016/j.ab.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/06/2015] [Accepted: 09/07/2015] [Indexed: 01/04/2023]
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Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection. Cancers (Basel) 2015; 7:1313-32. [PMID: 26193321 PMCID: PMC4586770 DOI: 10.3390/cancers7030837] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 01/15/2023] Open
Abstract
The molecular characterization of tumors using next generation sequencing (NGS) is an emerging diagnostic tool that is quickly becoming an integral part of clinical decision making. Cancer genomic profiling involves significant challenges including DNA quality and quantity, tumor heterogeneity, and the need to detect a wide variety of complex genetic mutations. Most available comprehensive diagnostic tests rely on primer based amplification or probe based capture methods coupled with NGS to detect hotspot mutation sites or whole regions implicated in disease. These tumor panels utilize highly customized bioinformatics pipelines to perform the difficult task of accurately calling cancer relevant alterations such as single nucleotide variations, small indels or large genomic alterations from the NGS data. In this review, we will discuss the challenges of solid tumor assay design/analysis and report a case study that highlights the need to include complementary technologies (i.e., arrays) and germline analysis in tumor testing to reliably identify copy number alterations and actionable variants.
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45
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Lamy PJ, Castan F, Lozano N, Montélion C, Audran P, Bibeau F, Roques S, Montels F, Laberenne AC. Next-Generation Genotyping by Digital PCR to Detect and Quantify the BRAF V600E Mutation in Melanoma Biopsies. J Mol Diagn 2015; 17:366-73. [PMID: 25952101 DOI: 10.1016/j.jmoldx.2015.02.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/21/2015] [Accepted: 02/18/2015] [Indexed: 12/27/2022] Open
Abstract
The detection of the BRAF V600E mutation in melanoma samples is used to select patients who should respond to BRAF inhibitors. Different techniques are routinely used to determine BRAF status in clinical samples. However, low tumor cellularity and tumor heterogeneity can affect the sensitivity of somatic mutation detection. Digital PCR (dPCR) is a next-generation genotyping method that clonally amplifies nucleic acids and allows the detection and quantification of rare mutations. Our aim was to evaluate the clinical routine performance of a new dPCR-based test to detect and quantify BRAF mutation load in 47 paraffin-embedded cutaneous melanoma biopsies. We compared the results obtained by dPCR with high-resolution melting curve analysis and pyrosequencing or with one of the allele-specific PCR methods available on the market. dPCR showed the lowest limit of detection. dPCR and allele-specific amplification detected the highest number of mutated samples. For the BRAF mutation load quantification both dPCR and pyrosequencing gave similar results with strong disparities in allele frequencies in the 47 tumor samples under study (from 0.7% to 79% of BRAF V600E mutations/sample). In conclusion, the four methods showed a high degree of concordance. dPCR was the more-sensitive method to reliably and easily detect mutations. Both pyrosequencing and dPCR could quantify the mutation load in heterogeneous tumor samples.
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Affiliation(s)
- Pierre-Jean Lamy
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France; Department of Biobank, Institut Régional du Cancer de Montpellier, Montpellier, France.
| | - Florence Castan
- Department of Statistics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Nicolas Lozano
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Cécile Montélion
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Patricia Audran
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Frédéric Bibeau
- Department of Biobank, Institut Régional du Cancer de Montpellier, Montpellier, France; Department of Pathology, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Sylvie Roques
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Frédéric Montels
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Anne-Claire Laberenne
- Department of Biology and Oncogenetics, Institut Régional du Cancer de Montpellier, Montpellier, France
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Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients. Nat Med 2015; 21:795-801. [PMID: 26030179 DOI: 10.1038/nm.3870] [Citation(s) in RCA: 617] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/30/2015] [Indexed: 02/07/2023]
Abstract
Colorectal cancers (CRCs) evolve by a reiterative process of genetic diversification and clonal evolution. The molecular profile of CRC is routinely assessed in surgical or bioptic samples. Genotyping of CRC tissue has inherent limitations; a tissue sample represents a single snapshot in time, and it is subjected to spatial selection bias owing to tumor heterogeneity. Repeated tissue samples are difficult to obtain and cannot be used for dynamic monitoring of disease progression and response to therapy. We exploited circulating tumor DNA (ctDNA) to genotype colorectal tumors and track clonal evolution during treatment with the epidermal growth factor receptor (EGFR)-specific antibodies cetuximab or panitumumab. We identified alterations in ctDNA of patients with primary or acquired resistance to EGFR blockade in the following genes: KRAS, NRAS, MET, ERBB2, FLT3, EGFR and MAP2K1. Mutated KRAS clones, which emerge in blood during EGFR blockade, decline upon withdrawal of EGFR-specific antibodies, indicating that clonal evolution continues beyond clinical progression. Pharmacogenomic analysis of CRC cells that had acquired resistance to cetuximab reveals that upon antibody withdrawal KRAS clones decay, whereas the population regains drug sensitivity. ctDNA profiles of individuals who benefit from multiple challenges with anti-EGFR antibodies exhibit pulsatile levels of mutant KRAS. These results indicate that the CRC genome adapts dynamically to intermittent drug schedules and provide a molecular explanation for the efficacy of rechallenge therapies based on EGFR blockade.
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Danese E, Minicozzi AM, Benati M, Montagnana M, Paviati E, Salvagno GL, Lima-Oliveira G, Gusella M, Pasini F, Lippi G, Guidi GC. Comparison of genetic and epigenetic alterations of primary tumors and matched plasma samples in patients with colorectal cancer. PLoS One 2015; 10:e0126417. [PMID: 25946211 PMCID: PMC4422441 DOI: 10.1371/journal.pone.0126417] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
Abstract
Background Although recent advances in circulating DNA analysis allow the prediction of tumor genomes by noninvasive means, some challenges remain, which limit the widespread introduction of cfDNA in cancer diagnostics. We analyzed the status of the two best characterized colorectal cancer (CRC) genetic and epigenetic alterations in a cohort of CRC patients, and then compared the degree to which the two patterns move from tissue to plasma in order to improve our understanding of biology modulating the concordance between tissues and plasma methylation and mutation profiles. Methods Plasma and tumor tissues were collected from 85 patients (69±14 years, 56 males). KRAS and SEPT9 status was assessed by allele refractory mutation system quantitative PCR and quantitative methylation-specific PCR, respectively. Six of the most common point mutations at codon 12 and 13 were investigated for KRAS analysis. Results KRAS mutations and SEPT9 promoter methylation were present in 34% (29/85) and in 82% (70/85) of primary tumor tissue samples. Both genetic and epigenetic analyses of cfDNA revealed a high overall concordance and specificity compared with tumor-tissue analyses. Patients presenting with both genetic and epigenetic alterations in tissue specimens (31.8%, 27/85) were considered for further analyses. The median methylation rates in tumour tissues and plasma samples were 64.5% (12.2–99.8%) and 14.5% (0–45.5%), respectively. The median KRAS mutation load (for matched mutations) was 33.6% (1.8–86.3%) in tissues and 2.9% (0–17.3) in plasma samples. The plasma/tissue (p/t) ratio of SEPT9 methylation rate was significantly higher than the p/t ratio of KRAS mutation load, especially in early stage cancers (p=0.0108). Conclusion The results of this study show a discrepant rate of epigenetic vs. genetic alterations moving from tissue to plasma. Many factors could affect mutation cfDNA analysis, including both presence of tumor clonal heterogeneity and strict compartmentalization of KRAS mutation profile. The present study highlights the importance of considering the nature of the alteration when analyzing tumor-derived cfDNA.
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Affiliation(s)
- Elisa Danese
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
- * E-mail:
| | - Anna Maria Minicozzi
- National Centre for Bowel Research and Surgical Innovation (NCBRSI), Academic Surgical Unit, Barts and The London NHS Trust, Queen Mary University of London, London, United Kingdom
| | - Marco Benati
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Martina Montagnana
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Elisa Paviati
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Gian Luca Salvagno
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Gabriel Lima-Oliveira
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Milena Gusella
- Oncology Department, Laboratory of Pharmacology and Molecular Biology, Rovigo General Hospital, Trecenta, Rovigo, Italy
| | - Felice Pasini
- Department of Medical Oncology, Rovigo Hospital, Rovigo, Italy
| | - Giuseppe Lippi
- Laboratory of Clinical Chemistry and Hematology, Academic Hospital of Parma, Parma, Italy
| | - Gian Cesare Guidi
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
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Steinbach C, Steinbrücker C, Pollok S, Walther K, Clement JH, Chen Y, Petersen I, Cialla-May D, Weber K, Popp J. KRAS mutation screening by chip-based DNA hybridization--a further step towards personalized oncology. Analyst 2015; 140:2747-54. [PMID: 25706807 DOI: 10.1039/c4an02086c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of predictive biomarkers can help to improve therapeutic options for the individual cancer patient. For the treatment of colon cancer patients with anti-EGFR-based drugs, the KRAS mutation status has to be determined to pre-select responders that will benefit from this medication. Amongst others, array-based tests have been established for profiling of the KRAS mutation status. Within this article we describe an on-chip hybridization technique to screen therapeutic relevant KRAS codon 12 mutations. The DNA chip-based platform enables the reliable discrimination of selected mutations by allele-specific hybridization. Here, silver deposits represent robust endpoint signals that allow for a simple naked eye rating. With the here presented assay concept a precise identification of heterozygous and homozygous KRAS mutations, even against a background of up to 95% wild-type DNA, was realizable. The applicability of the test was successfully proven for various cancer cell lines as well as clinical tumour samples. Thus, the chip-based DNA hybridization technique seems to be a promising tool for KRAS mutation analysis to further improve personalized cancer treatment.
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Affiliation(s)
- Christine Steinbach
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany
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Atsumi J, Hanami T, Enokida Y, Ogawa H, Delobel D, Mitani Y, Kimura Y, Soma T, Tagami M, Takase Y, Ichihara T, Takeyoshi I, Usui K, Hayashizaki Y, Shimizu K. Eprobe-mediated screening system for somatic mutations in the KRAS locus. Oncol Rep 2015; 33:2719-27. [PMID: 25823645 PMCID: PMC4431451 DOI: 10.3892/or.2015.3883] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/03/2015] [Indexed: 12/21/2022] Open
Abstract
Activating mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) loci are largely predictive of resistance to epidermal growth factor receptor (EGFR) therapy in colorectal cancer (CRC). A highly sensitive detection system for the KRAS gene mutations is urgently needed; however, conventional methods have issues with feasibility and cost performance. Here, we describe a novel detection system using a fluorescence ‘Eprobe’ capable of detecting low level KRAS gene mutations, via real-time PCR, with high sensitivity and simple usability. We designed our Eprobes to be complementary to wild-type (WT) KRAS or to the commonly mutated codons 12 and 13. The WT Eprobe binds strongly to the WT DNA template and suppresses amplification by blocking annealing of the primer during PCR. Eprobe-PCR with WT Eprobe shows high sensitivity (0.05–0.1% of plasmid DNA, 1% of genomic DNA) for the KRAS mutation by enrichment of the mutant type (MT) amplicon. Assay performance was compared to Sanger sequencing using 92 CRC samples. Discrepancies were analyzed by mutation genotyping via Eprobe-PCR with full match Eprobes for 7 prevalent mutations and the next generation sequencing (NGS). Significantly, the Eprobe system had a higher sensitivity for detecting KRAS mutations in CRC patient samples; these mutations could not be identified by Sanger sequencing. Thus, the Eprobe approach provides for highly sensitive and convenient mutation detection and should be useful for diagnostic applications.
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Affiliation(s)
- Jun Atsumi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takeshi Hanami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasuaki Enokida
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hiroomi Ogawa
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Diane Delobel
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Mitani
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Kimura
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Takahiro Soma
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Michihira Tagami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshiaki Takase
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tatsuo Ichihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Izumi Takeyoshi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Kimihiro Shimizu
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
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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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