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Chen N, He L, Zou Q, Deng H. HER2 targeted therapy in colorectal Cancer: Current landscape and future directions. Biochem Pharmacol 2024; 223:116101. [PMID: 38442793 DOI: 10.1016/j.bcp.2024.116101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/11/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer (CRC) is one of the most common causes of tumor-related deaths globally. Despite recent improvements in the comprehensive therapy of malignancy, metastatic CRC continues to have a poor prognosis. Human epidermal growth factor receptor 2 (HER2) is an established oncogenic driver, which is successfully targeted for breast and gastric cancers. Approximately 5% of CRC patients carry somatic HER2 mutations or gene amplification. In 2019, the U.S. Food and Drug Administration have approved trastuzumab and pertuzumab in combination with chemotherapy for the treatment of HER2-positive metastatic CRC. This approval marked a significant milestone in the treatment of CRC, as HER2-positive patients now have access to targeted therapies that can improve their outcomes. Yet, assessment for HER2 overexpression/ amplification in CRC has not been standardized. The resistance mechanisms to anti-HER2 therapy have been not clearly investigated in CRC. Although many unknowns remain, an improved understanding of these anti-HER2 agents will be essential for advanced CRC. In this review, we provide an overview of the role of HER2 in CRC as an oncogenic driver, a prognostic and predictive biomarker, and a clinically actionable target, as well as the current progress and challenges in the field.
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Affiliation(s)
- Na Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China; Center of Science and Research, Chengdu Medical College, Chengdu, 610500, China
| | - Ling He
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qiang Zou
- Center of Science and Research, Chengdu Medical College, Chengdu, 610500, China.
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China.
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2
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Alsolme E, Alqahtani S, Fageeh M, Barakeh D, Sharma NK, Mangul S, Robinson HA, Fathaddin A, Hauser CAE, Abedalthagafi M. The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel. Diagnostics (Basel) 2023; 13:2993. [PMID: 37761360 PMCID: PMC10527739 DOI: 10.3390/diagnostics13182993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. PATIENTS AND METHODS We analyzed the mutation frequencies of common actionable genes and their association with clinicopathological characteristics and oncologic outcomes using targeted NGS in 107 Saudi Arabian patients without a family history of CRC. RESULTS Approximately 98% of patients had genetic alterations. Frequent mutations were observed in BRCA2 (79%), CHEK1 (78%), ATM (76%), PMS2 (76%), ATR (74%), and MYCL (73%). The APC gene was not included in the panel. Statistical analysis using the Cox proportional hazards model revealed an unusual positive association between poorly differentiated tumors and survival rates (p = 0.025). Although no significant univariate associations between specific mutations or overall mutation rate and overall survival were found, our preliminary analysis of the molecular markers for CRC in a predominantly Arab population can provide insights into the molecular pathways that play a significant role in the underlying disease progression. CONCLUSIONS These results may help optimize personalized therapy when drugs specific to a patient's mutation profile have already been developed.
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Affiliation(s)
- Ebtehal Alsolme
- Genomic Research Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia; (E.A.); (D.B.)
| | - Saleh Alqahtani
- Royal Clinic and Hepatology Department, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
| | - Musa Fageeh
- Pathology Department, King Saud Medical City, Riyadh 12746, Saudi Arabia;
| | - Duna Barakeh
- Genomic Research Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia; (E.A.); (D.B.)
| | - Nitesh K. Sharma
- The Titus Family Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90007, USA; (N.K.S.); (S.M.)
| | - Serghei Mangul
- The Titus Family Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90007, USA; (N.K.S.); (S.M.)
| | | | - Amany Fathaddin
- Department of Pathology, Collage of Medicine, King Saud University, Riyadh 11362, Saudi Arabia;
| | - Charlotte A. E. Hauser
- Laboratory for Nanomedicine, Biological & Environmental Science & Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA 30307, USA
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Emerging Role of ERBB2 in Targeted Therapy for Metastatic Colorectal Cancer: Signaling Pathways to Therapeutic Strategies. Cancers (Basel) 2022; 14:cancers14205160. [PMID: 36291943 PMCID: PMC9600272 DOI: 10.3390/cancers14205160] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the second most common cause of cancer-related mortality worldwide. Currently available targeted therapies for metastatic CRC mainly target vascular endothelial growth factor and epidermal growth factor receptor in RAS wild-type tumors. Although Erb-B2 receptor tyrosine kinase 2 (ERBB2/human epidermal growth factor receptor 2) plays a significant therapeutic role in breast and gastric cancers, there are no licensed ERBB2-targeted therapies for metastatic CRC. This review aims to outline the molecular biology of ERBB2-positive metastatic CRC and potential targeted therapeutic strategies. Abstract Despite recent improvements in the comprehensive therapy of malignancy, metastatic colorectal cancer (mCRC) continues to have a poor prognosis. Notably, 5% of mCRC cases harbor Erb-B2 receptor tyrosine kinase 2 (ERBB2) alterations. ERBB2, commonly referred to as human epidermal growth factor receptor 2, is a member of the human epidermal growth factor receptor family of protein tyrosine kinases. In addition to being a recognized therapeutic target in the treatment of gastric and breast malignancies, it is considered crucial in the management of CRC. In this review, we describe the molecular biology of ERBB2 from the perspective of biomarkers for mCRC-targeted therapy, including receptor structures, signaling pathways, gene alterations, and their detection methods. We also discuss the relationship between ERBB2 aberrations and the underlying mechanisms of resistance to anti-EGFR therapy and immunotherapy tolerance in these patients with a focus on novel targeted therapeutics and ongoing clinical trials. This may aid the development of a new standard of care in patients with ERBB2-positive mCRC.
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Chang YK, Tseng HH, Leung CM, Lu KC, Tsai KW. Targeted Next-Generation Sequencing-Based Multiple Gene Mutation Profiling of Patients with Rectal Adenocarcinoma Receiving or Not Receiving Neoadjuvant Chemoradiotherapy. Int J Mol Sci 2022; 23:ijms231810353. [PMID: 36142267 PMCID: PMC9499649 DOI: 10.3390/ijms231810353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
This study investigated whether oncogenic and tumor-suppressive gene mutations are involved in the differential outcomes of patients with rectal carcinoma receiving neoadjuvant chemoradiotherapy (nCRT). Genomic DNA was obtained from formalin-fixed paraffin-embedded (FFPE) specimens of patients with rectal carcinoma who received a complete nCRT course. Gene mutation status was examined in specimens from patients before and after nCRT by using the AmpliSeq platform. Our data revealed that the nonsynonymous p53, APC, KRAS, CDKN2A, and EGFR mutations were observed in 93.1%, 65.5%, 48.6%, and 31% of the patients with rectal adenocarcinoma, respectively. BRAF, FBXW7, PTEN, and SMAD4 mutations were observed in 20.7% of patients with rectal carcinoma. The following 12 gene mutations were observed more frequently in the patients exhibiting a complete response than in those demonstrating a poor response before nCRT: ATM, BRAF, CDKN2A, EGFR, FLT3, GNA11, KDR, KIT, PIK3CA, PTEN, PTPN11, SMAD4, and TP53. In addition, APC, BRAF, FBXW7, KRAS, SMAD4, and TP53 mutations were retained after nCRT. Our results indicate a complex mutational profile in rectal carcinoma, suggesting the involvement of BRAF, SMAD4, and TP53 genetic variants in the outcomes of patients with nCRT.
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Affiliation(s)
- You-Kang Chang
- Department of Radiation Oncology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei 23142, Taiwan
- College of Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Hui-Hwa Tseng
- Department of Anatomic Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 97004, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 81341, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 97004, Taiwan
- Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City 24205, Taiwan
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 23142, Taiwan
- Correspondence: ; Tel.: +886-2-266289779 (ext. 5796); Fax: +886-2-66281258
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Alborelli I, Jermann PM. Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis. Methods Mol Biol 2022; 2493:331-351. [PMID: 35751825 DOI: 10.1007/978-1-0716-2293-3_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Broad molecular profiling by next-generation sequencing of solid tumors has become a critical tool for clinical decision-making in the era of precision oncology. In addition to many already approved targeted therapies, more than half of ongoing oncology-related clinical trials are biomarker-driven. Therefore, accurate and reliable assays are needed to assess the genetic make-up of tumor cells and guide clinicians in the therapy decision process. In order to obtain high-quality NGS data for variant detection, certain preanalytical steps and quality metrics should be followed. These include assessment of sample types, choice of extraction method, library preparation technology, sequencing platform, and finally sequencing quality control. Each of these steps has certain challenges and pitfalls that need to be addressed and overcome, respectively. In this chapter, we address the preanalytical quality control and how each of the involved steps may influence the final result. Following these guidelines and QC metrics may help in obtaining optimal results that will allow the precise and robust assessment of genetic variants in a clinical setting.
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Affiliation(s)
- Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Philip M Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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Epistolio S, Cefalì M, Spina P, Molinari F, Movilia A, Cergnul M, Mazzucchelli L, De Dosso S, Frattini M, Saletti P. Occurence of RAS reversion in metastatic colorectal cancer patients treated with bevacizumab. Oncotarget 2021; 12:1046-1056. [PMID: 34084279 PMCID: PMC8169066 DOI: 10.18632/oncotarget.27965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/03/2021] [Indexed: 12/22/2022] Open
Abstract
Background: A disappearance of RAS mutations in the plasma of about 50% of mCRCs (metastatic colorectal cancers) treated with bevacizumab-based chemotherapy has been reported. Our aim was to evaluate the same issue at tissue level. Materials and Methods: Using next-generation sequencing and real-time PCR approaches, we characterized the primary tumor (PT) and paired liver metastases in 28 RAS mutant mCRCs. Patients were subdivided into 3 treatment groups: 1) bevacizumab plus chemotherapy; 2) chemotherapy alone; 3) any systemic therapy (control group). In groups 1 and 2, liver metastases were resected after removal of PT and subsequent neoadjuvant systemic therapy. Results: RAS mutant alleles are at the same percentage in PT and liver metastases in the control group, while a significant reduction of the level of RAS mutations was detected in 57.1% of cases in group 1 and in 8.3% of cases in group 2. Differences among groups are statistically significant (p = 0.038). Conclusions: Most of mCRC patients treated with bevacizumab-containing regimens experience a strong reduction of RAS mutant cells, suggesting bevacizumab as particularly active against RAS mutant cells. This finding might have potential therapeutic implications, as anti-EGFR could be reconsidered in primarily RAS mutant patients reverted to a wild-type status after bevacizumab exposure.
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Affiliation(s)
- Samantha Epistolio
- Institute of Pathology, EOC, Locarno, Switzerland.,These authors are Joined First Authors
| | - Marco Cefalì
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland.,These authors are Joined First Authors
| | - Paolo Spina
- Institute of Pathology, EOC, Locarno, Switzerland.,Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | | | - Alessandra Movilia
- Department of Pathology, ASST Ovest Milanese, Ospedale di Legnano, Legnano, Italy
| | - Massimiliano Cergnul
- Department of Medical Oncology, ASST Ovest Milanese, Ospedale di Legnano, Legnano, Italy
| | | | - Sara De Dosso
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland
| | - Milo Frattini
- Institute of Pathology, EOC, Locarno, Switzerland.,These authors are Joint Senior Authors
| | - Piercarlo Saletti
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland.,Current address: Department of Medical Oncology, Clinica Luganese Moncucco, Lugano, Switzerland.,These authors are Joint Senior Authors
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8
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Ye J, Lin M, Zhang C, Zhu X, Li S, Liu H, Yin J, Yu H, Zhu K. Tissue gene mutation profiles in patients with colorectal cancer and their clinical implications. Biomed Rep 2020; 13:43-48. [PMID: 32440349 DOI: 10.3892/br.2020.1303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/03/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer in the world, and targeted therapy is frequently used in the clinical management of the disease. A complete and accurate picture of tissue gene mutations is therefore critical. Tissue specimens from 117 patients with CRC were used for high throughput DNA next-generation sequencing (NGS) analysis. Hotspots from 50 genes frequently associated with the development and progression of solid tumors were targeted for sequencing. Characterization of tissue gene mutations was performed; the tissue mutation positive rates of KRAS, KIT, PIK3CA, MET and EGFR were 52.1, 19.7, 29.9, 15.4 and 14.5%, respectively. The mutation positive rates of TP53, APC, CDKN2A, STK11 and FBXW7 were 65.8, 39.3, 32.5, 19.7 and 19.7%, respectively. The most frequent KRAS mutations were G12A/C/D/S/V, accounting for 61.2% of all KRAS mutations. The most frequent TP53 mutations were R273C/G/H/L, accounting for 8.5% of all TP53 mutations. The most frequent APC mutation was E1554fs, accounting for 19.7% of all APC mutations. IDH1 R132C/H, KIT M541L, MET N375S, and SMAD4 R361C/H were also frequently identified. TP53 mutations were more common in patients ≥60 years old (P<0.05), and IDH1 mutations were more common in male patients (P<0.05). NGS 50 gene panel sequencing provides a comprehensive tissue gene mutation profile which may significantly improve clinical management.
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Affiliation(s)
- Jun Ye
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Mei Lin
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Chuanmeng Zhang
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Xiaowei Zhu
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Sumeng Li
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Hui Liu
- Xuzhou Medical University, Department of Pathology, Xuzhou, Jiangsu 221000, P.R. China
| | - Jianfeng Yin
- Jianwei Medical Laboratory, Taizhou, Jiangsu 225300, P.R. China
| | - Hong Yu
- Taizhou People's Hospital, The Center for Translational Medicine, Taizhou, Jiangsu 225300, P.R. China
| | - Kuichun Zhu
- R&D Department, Labway Clinical Laboratories, Shanghai 210000, P.R. China.,R&D Department, Wuxi Shenrui Bio-Pharmaceuticals Co., Ltd., Wuxi, Jiangsu 214000, P.R. China
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9
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Garg S, Grenier S, Misyura M, Sukhai MA, Thomas M, Kamel-Reid S, Stockley T. Assessing the Diagnostic Yield of Targeted Next-Generation Sequencing for Melanoma and Gastrointestinal Tumors. J Mol Diagn 2020; 22:467-475. [PMID: 32036084 DOI: 10.1016/j.jmoldx.2019.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/19/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
A common rationale in molecular diagnostic laboratories is that implementation of next-generation sequencing (NGS) enables simultaneous multigene testing, allowing increased information benefit compared with non-NGS assays. However, minimal published data exist to support this justification. The current study compared clinical diagnostic yield of TruSight Tumor 26 Sequencing Panel (TST26) in melanoma, colorectal (CRC), and gastrointestinal stromal (GIST) tumors with non-NGS assays. A total of 1041 formalin-fixed, paraffin-embedded tumors, of melanoma, CRC, and GIST, were profiled. NGS results were compared with non-NGS single-gene or single-variant assays with respect to variant output and diagnostic yield. A total of 79% melanoma and 94% CRC tumors were variant positive by panel testing. TST26 panel improved serine/threonine-protein kinase B-raf (BRAF) variant detection in melanoma compared with single-variant BRAF Val600Glu/Lys (V600E/K) routine tests by 24% and detected variants in genes other than BRAF, NRAS, and KIT, which could impact patient management in 20% additional cases. NGS enhanced diagnostic yield in CRC by 36% when compared with routine single-gene assays. In contrast, no added benefit of NGS-based testing for GIST tumors was observed. TST26 panel either missed or inaccurately called complex insertion/deletion variants in KIT exon 11, which were accurately identified by non-NGS methods. Findings of this study demonstrate the differential impact of cancer site and variant type on diagnostic test information yield from NGS assays.
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Affiliation(s)
- Swati Garg
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Sylvie Grenier
- Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Maksym Misyura
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Mahadeo A Sukhai
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Mariam Thomas
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario; Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tracy Stockley
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario; Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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10
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Kofanova O, Bellora C, Garcia Frasquilho S, Antunes L, Hamot G, Mathay C, Mommaerts K, Muller A, DeWitt B, Betsou F. Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses. N Biotechnol 2020; 54:52-61. [DOI: 10.1016/j.nbt.2019.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/24/2019] [Accepted: 07/28/2019] [Indexed: 12/25/2022]
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11
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Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma. Sci Rep 2019; 9:13995. [PMID: 31570735 PMCID: PMC6769015 DOI: 10.1038/s41598-019-50171-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.
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12
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Parker JDK, Yap SQ, Starks E, Slind J, Swanson L, Docking TR, Fuller M, Zhou C, Walker B, Filipenko D, Xiong W, Karimuddin AA, Phang PT, Raval M, Brown CJ, Karsan A. Fixation Effects on Variant Calling in a Clinical Resequencing Panel. J Mol Diagn 2019; 21:705-717. [PMID: 31055024 DOI: 10.1016/j.jmoldx.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 11/16/2022] Open
Abstract
Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.
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Affiliation(s)
- Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Shyong Quin Yap
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Elizabeth Starks
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jillian Slind
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Lucas Swanson
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chen Zhou
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair Walker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Douglas Filipenko
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Wei Xiong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Ahmer A Karimuddin
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - P Terry Phang
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Manoj Raval
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Carl J Brown
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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13
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Naito Y, Takahashi H, Shitara K, Okamoto W, Bando H, Kuwata T, Kuboki Y, Matsumoto S, Miki I, Yamanaka T, Watanabe A, Kojima M. Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study. Jpn J Clin Oncol 2018; 48:559-564. [PMID: 29659903 PMCID: PMC5974784 DOI: 10.1093/jjco/hyy052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/05/2018] [Indexed: 01/08/2023] Open
Abstract
Background To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. Methods Patients with unresectable, advanced, or recurrent solid tumors were included. Key eligibility criteria were as follows: 20 years or older, any planned systemic therapy, adequate lesion for biopsy, and written informed consent. Samples were fixed in 10% buffered formalin and embedded in paraffin. Cancer-derived DNA was extracted, and amplicon sequencing was performed using Ion AmpliseqTM Cancer Hotspot Panel version 1.0 or version 2.0 by central vendor. We evaluated the success rate of sequencing, and the proportion of the patients with actionable mutations. We organized an expert panel to share the results of targeted sequence, make annotations and reports, and discuss concomitant ethical/legal/social issues. Results A total of 232 patients were included, and 208 were successfully analyzed (success rate of 89.7%). The biopsy procedures were safe, with only one case of Grade 3 vasovagal reaction. The proportion of actionable/druggable mutations was 38.9% (81/208), which was not significantly different between the cancer panel version 1.0 and version 2.0 (P = 0.476). Expert panel could discuss the findings and make sufficient reports. Conclusions We confirmed the feasibility of NGS-based amplicon sequencing using biopsy samples, making the basis for nationwide genome screening for cancer patients using biopsy samples. Our results suggest that focused panel may be sufficient to detect major mutations.
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Affiliation(s)
- Yoichi Naito
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Hideaki Takahashi
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Kohei Shitara
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Wataru Okamoto
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Hideaki Bando
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Takeshi Kuwata
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Yasutoshi Kuboki
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Shingo Matsumoto
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Izumi Miki
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | | | | | - Motohiro Kojima
- National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
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14
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Wang Y, Liu H, Hou Y, Zhou X, Liang L, Zhang Z, Shi H, Xu S, Hu P, Zheng Z, Liu R, Tang T, Ye F, Liang Z, Bu H. Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients. Virchows Arch 2018; 472:959-968. [PMID: 29705968 DOI: 10.1007/s00428-018-2359-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/01/2018] [Accepted: 04/08/2018] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) has become a promising approach for tumor somatic mutation detection. However, stringent validation is required for its application on clinical specimens, especially for low-quality formalin-fixed paraffin-embedded (FFPE) tissues. Here, we validated the performance of an amplicon-based targeted NGS assay, OncoAim™ DNA panel, on both commercial reference FFPE samples and clinical FFPE samples of Chinese colorectal cancer (CRC) patients. Then we profiled the mutation spectrum of 648 Chinese CRC patients in a multicenter study to explore its clinical utility. This NGS assay achieved 100% test specificity and 95-100% test sensitivity for variants with mutant allele frequency (MAF) ≥ 5% when median read depth ≥ 500×. The orthogonal methods including amplification refractory mutation system (ARMS)-PCR and Sanger sequencing validated that NGS generated three false negatives (FNs) but no false positives (FPs) among 516 clinical samples for KRAS aberration detection. Genomic profiling of Chinese CRC patients with this assay revealed that 63.3% of the tumors harbored clinically actionable alterations. Besides the commonly mutated genes including TP53 (52.82%), KRAS (46.68%), APC (24.09%), PIK3CA (18.94%), SMAD4 (9.47%), BRAF (6.15%), FBXW7 (5.32%), and NRAS (4.15%), other less frequently mutated genes were also identified. Statistically significant association of specific mutated genes with certain clinicopathological features was detected, e.g., both BRAF and PIK3CA were more prevalent in right-side CRC (p < 0.001 and p = 0.002, respectively). We concluded this targeted NGS assay is qualified for clinical practice, and our findings could help the diagnosis and prognosis of Chinese CRC patients.
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Affiliation(s)
- Yajian Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haijing Liu
- Department of Pathology, Peking University Third Hospital, Beijing, 100000, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Li Liang
- Huayin Laboratory, Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Zhang
- Department of Pathology, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Huaiyin Shi
- Department of Pathology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, 100000, China
| | - Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Peizhen Hu
- Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Zuyu Zheng
- Singlera Genomics Inc., Shanghai, 201318, China
| | - Rui Liu
- Singlera Genomics Inc., Shanghai, 201318, China
| | | | - Feng Ye
- Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China. .,Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hong Bu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China
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15
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Ross JS, Fakih M, Ali SM, Elvin JA, Schrock AB, Suh J, Vergilio J, Ramkissoon S, Severson E, Daniel S, Fabrizio D, Frampton G, Sun J, Miller VA, Stephens PJ, Gay LM. Targeting HER2 in colorectal cancer: The landscape of amplification and short variant mutations in ERBB2 and ERBB3. Cancer 2018; 124:1358-1373. [PMID: 29338072 PMCID: PMC5900732 DOI: 10.1002/cncr.31125] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND In contrast to lung cancer, few precision treatments are available for colorectal cancer (CRC). One rapidly emerging treatment target in CRC is ERBB2 (human epidermal growth factor receptor 2 [HER2]). Oncogenic alterations in HER2, or its dimerization partner HER3, can underlie sensitivity to HER2-targeted therapies. METHODS In this study, 8887 CRC cases were evaluated by comprehensive genomic profiling for genomic alterations in 315 cancer-related genes, tumor mutational burden, and microsatellite instability. This cohort included both colonic (7599 cases; 85.5%) and rectal (1288 cases; 14.5%) adenocarcinomas. RESULTS A total of 569 mCRCs were positive for ERBB2 (429 cases; 4.8%) and/or ERBB3 (148 cases; 1.7%) and featured ERBB amplification, short variant alterations, or a combination of the 2. High tumor mutational burden (≥20 mutations/Mb) was significantly more common in ERBB-mutated samples, and ERBB3-mutated CRCs were significantly more likely to have high microsatellite instability (P<.002). Alterations affecting KRAS (27.3%) were significantly underrepresented in ERBB2-amplified samples compared with wild-type CRC samples (51.8%), and ERBB2- or ERBB3-mutated samples (49.0% and 60.8%, respectively) (P<.01). Other significant differences in mutation frequency were observed for genes in the PI3K/MTOR and mismatch repair pathways. CONCLUSIONS Although observed less often than in breast or upper gastrointestinal carcinomas, indications for which anti-HER2 therapies are approved, the percentage of CRC with ERBB genomic alterations is significant. Importantly, 32% of ERBB2-positive CRCs harbor short variant alterations that are undetectable by routine immunohistochemistry or fluorescence in situ hybridization testing. The success of anti-HER2 therapies in ongoing clinical trials is a promising development for patients with CRC. Cancer 2018;124:1358-73. © 2018 Foundation Medicine, Inc. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society.
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Affiliation(s)
- Jeffrey S. Ross
- Foundation Medicine IncCambridgeMassachusetts
- Department of PathologyAlbany Medical CenterAlbanyNew York
| | - Marwan Fakih
- Department of Medical Oncology and Therapeutics Research City of HopeDuarteCalifornia
| | | | | | | | - James Suh
- Foundation Medicine IncCambridgeMassachusetts
| | | | | | | | | | | | | | - James Sun
- Foundation Medicine IncCambridgeMassachusetts
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16
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Bartels S, Schipper E, Hasemeier B, Kreipe H, Lehmann U. Routine clinical mutation profiling using next generation sequencing and a customized gene panel improves diagnostic precision in myeloid neoplasms. Oncotarget 2017; 7:30084-93. [PMID: 27029036 PMCID: PMC5058665 DOI: 10.18632/oncotarget.8310] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/14/2016] [Indexed: 01/08/2023] Open
Abstract
Microscopic examination of myelodysplastic syndromes (MDS) and myelodysplastic-myeloproliferative neoplasms (MDS/MPN) may be challenging because morphological features can overlap with those of reactive states. Demonstration of clonal hematopoiesis provides a diagnostic clue and has become possible by comprehensive mutation profiling of a number of frequently mutated genes, some of them with large coding regions. To emphasize the potential benefit of NGS in hematopathology we present sequencing results from routinely processed formalin-fixed and paraffin-embedded (FFPE) bone marrow trephines (n = 192). A customized amplicon-based gene panel including 23 genes frequently mutated in myeloid neoplasms was established and implemented. Thereby, 629,691 reads per sample (range 179,847–1,460,412) and a mean coverage of 2,702 (range 707–6,327) could be obtained, which are sufficient for comprehensive mutational profiling. Seven samples failed in sequencing (3.6%). In 185 samples we found in total 269 pathogenic variants (mean 1.4 variants per patient, range 0-5), 125 Patients exhibit at least one pathogenic mutation (67.6%). Variants show allele frequencies ranging from 6.7% up to 95.7%. Most frequently mutated genes were TET2 (28.7%), SRSF2 (19.5%), ASXL1 (8.6%) and U2AF1 (8.1%). The mutation profiling increases the diagnostic precision and adds prognostic information.
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Affiliation(s)
- Stephan Bartels
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Elisa Schipper
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Britta Hasemeier
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
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17
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Hou H, Liu D, Zhang C, Jiang Y, Lu G, Zhou N, Yang X, Zhang X, Li Z, Zhu H, Qian Z, Zhang X. Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine. Oncotarget 2017; 8:105072-105080. [PMID: 29285234 PMCID: PMC5739621 DOI: 10.18632/oncotarget.21349] [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: 05/13/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. METHODS Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent. In total, 7708 exons of 508 tumor-related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, INDELs, copy number alterations, and gene fusions. RESULTS The study found that 50.9% (29/57) of the tumors harbored KRAS mutations, 3.5% (2/57) harbored NRAS mutations and 3.5% (2/57) harbored BRAF mutations. More specifically, 89.7% (26/29) of RAS mutations were located in codon 12. Except for RAS and RAF, anti-EGFR therapy response genetic mutations in PTEN (n=2) and PIK3CA (n=1) were found in 4.7% (3/64) of the samples. Actionable alterations were found in HER2 (n = 7), CCND2 (n = 2), NF1 (n = 1), and BRCA1 (n = 1). CONCLUSIONS Our results illustrated that 82.5% (47/57) of the samples harbored at least one actionable genetic alteration identified by NGS. HER2 amplifications or mutations, which were identified in 12.3% of the tissues, defined a unique molecular subtype of CRC. The study suggests that high-throughput NGS testing in CRC tissues is a comprehensive and efficient genomic profiling assay to guide personalized therapy.
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Affiliation(s)
- Helei Hou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Dong Liu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Chuantao Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Guifang Lu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Na Zhou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Xiaonan Yang
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Xiaoping Zhang
- Department of Clinical Laboratory, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhuokun Li
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xiaochun Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
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18
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Do H, Molania R, Mitchell PL, Vaiskunaite R, Murdoch JD, Dobrovic A. Reducing Artifactual EGFR T790M Mutations in DNA from Formalin-Fixed Paraffin-Embedded Tissue by Use of Thymine-DNA Glycosylase. Clin Chem 2017; 63:1506-1514. [DOI: 10.1373/clinchem.2017.271932] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/19/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines. We therefore investigated the use of thymine-DNA glycosylase (TDG) to reduce artifactual T790M mutations.
METHODS
Formalin-fixed normal lung tissues and lung squamous cell carcinomas were tested to measure the frequency of false-positive EGFR mutations by use of droplet digital PCR before and after treatment with either UDG or TDG. Methylation at the cytosine at EGFR T790 was assessed by pyrosequencing and by analysis of public databases.
RESULTS
Artifactual EGFR T790M mutations were detected in all of the archival formalin-fixed normal lung and lung squamous cell carcinomas at mutant allele frequencies of 1% or lower. The cytosine at EGFR T790 showed high levels of methylation in all lung cancer samples and normal tissues. Pretreatment of the formalin-fixed DNA with either UDG or TDG reduced the false EGFR T790M mutations, but a greater reduction was seen with the TDG treatment.
CONCLUSIONS
Both U:G and T:G lesions in formalin-fixed tissue are sources of false-positive EGFR T790M mutations. This is the first report of the use of TDG to reduce sequence artifacts in formalin-fixed DNA and is applicable to the accurate detection of mutations arising at methylated cytosines.
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Affiliation(s)
- Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Australia
- Department of Pathology, University of Melbourne, Melbourne, Australia
| | - Ramyar Molania
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Paul L Mitchell
- Department of Medical Oncology, Austin Health, Melbourne, Australia
| | | | | | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Australia
- Department of Pathology, University of Melbourne, Melbourne, Australia
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19
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Brait M, Izumchenko E, Kagohara LT, Long S, Wysocki PT, Faherty B, Fertig EJ, Khor TO, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D. Comparative mutational landscape analysis of patient-derived tumour xenografts. Br J Cancer 2017; 116:515-523. [PMID: 28118322 PMCID: PMC5318980 DOI: 10.1038/bjc.2016.450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted next-generation sequencing-based approaches offer promising diagnostic capabilities, there are still limitations. There is a pressing clinical need for a well-validated, rapid, cost-effective mutation profiling system in patient specimens. Given their speed and cost-effectiveness, quantitative PCR mutation detection techniques are well suited for the clinical environment. The qBiomarker mutation PCR array has high sensitivity and shorter turnaround times compared with other methods. However, a direct comparison with existing viable alternatives are required to assess its true potential and limitations. METHODS In this study, we evaluated a panel of 117 patient-derived tumour xenografts by the qBiomarker array and compared with other methods for mutation detection, including Ion AmpliSeq sequencing, whole-exome sequencing and droplet digital PCR. RESULTS Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics. CONCLUSIONS This large-scale direct comparison and validation of currently available mutation detection approaches is extremely relevant for the current scenario of precision medicine and will lead to informed choice of screening methodologies, especially in lower budget conditions or time frame limitations.
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Affiliation(s)
- Mariana Brait
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Luciane T Kagohara
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Samuel Long
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Piotr T Wysocki
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Brian Faherty
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Elana J Fertig
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Tin Oo Khor
- Champions Oncology, Baltimore, MD 21205, USA
| | | | - Gilson Baia
- Champions Oncology, Baltimore, MD 21205, USA
| | | | - Ido Sloma
- Champions Oncology, Baltimore, MD 21205, USA
| | - Ido Ben-Zvi
- Champions Oncology, Baltimore, MD 21205, USA
| | - Keren Paz
- Champions Oncology, Baltimore, MD 21205, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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20
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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21
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Shahsiah R, DeKoning J, Samie S, Latifzadeh SZ, Kashi ZM. Validation of a next generation sequencing panel for detection of hotspot cancer mutations in a clinical laboratory. Pathol Res Pract 2016; 213:98-105. [PMID: 28049581 DOI: 10.1016/j.prp.2016.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Abstract
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform. Important parameters for somatic mutations including the threshold for differentiation of a positive and a negative result, coverage, sensitivity, specificity, and limit of detection (LoD) were analyzed. Variant calls with coverage of <100x were found to be inaccurate. The limit of detection for identifying hotspot mutations was determined to be 4.3%. The sensitivity and specificity of the method were 96.1% and 97.8% respectively. No statistically significant difference was found between different gene targets in terms of performance of hotspot frequency measurement for the subset tested. In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation.
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Affiliation(s)
- Reza Shahsiah
- Cancer Research Center, Tehran University of Medical Sciences, Iran.
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22
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Fontanges Q, De Mendonca R, Salmon I, Le Mercier M, D'Haene N. Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers. Int J Mol Sci 2016; 17:ijms17122117. [PMID: 27999270 PMCID: PMC5187917 DOI: 10.3390/ijms17122117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 01/01/2023] Open
Abstract
Promising targeted therapy and personalized medicine are making molecular profiling of tumours a priority. For colorectal cancer (CRC) patients, international guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-epidermal growth factor receptor agents (anti-EGFR). Daily, new data emerge on the theranostic and prognostic role of molecular biomarkers, which is a strong incentive for a validated, sensitive and broadly available molecular screening test in order to implement and improve multi-modal therapy strategy and clinical trials. Next generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. Targeted NGS is a method that allows parallel sequencing of thousands of short DNA sequences in a single test offering a cost-effective approach for detecting multiple genetic alterations with a minimum amount of DNA. In the present review, we collected data concerning the clinical application of NGS technology in the setting of colorectal cancer.
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Affiliation(s)
- Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Ricardo De Mendonca
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
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Papadopoulou E, Metaxa-Mariatou V, Tsaousis G, Tsoulos N, Tsirigoti A, Efstathiadou C, Apessos A, Agiannitopoulos K, Pepe G, Bourkoula E, Nasioulas G. Molecular predictive markers in tumors of the gastrointestinal tract. World J Gastrointest Oncol 2016; 8:772-785. [PMID: 27895815 PMCID: PMC5108979 DOI: 10.4251/wjgo.v8.i11.772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/11/2016] [Accepted: 08/31/2016] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal malignancies are among the leading causes of cancer-related deaths worldwide. Like all human malignancies they are characterized by accumulation of mutations which lead to inactivation of tumor suppressor genes or activation of oncogenes. Advances in Molecular Biology techniques have allowed for more accurate analysis of tumors’ genetic profiling using new breakthrough technologies such as next generation sequencing (NGS), leading to the development of targeted therapeutical approaches based upon biomarker-selection. During the last 10 years tremendous advances in the development of targeted therapies for patients with advanced cancer have been made, thus various targeted agents, associated with predictive biomarkers, have been developed or are in development for the treatment of patients with gastrointestinal cancer patients. This review summarizes the advances in the field of molecular biomarkers in tumors of the gastrointestinal tract, with focus on the available NGS platforms that enable comprehensive tumor molecular profile analysis.
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Armengol G, Sarhadi VK, Ghanbari R, Doghaei-Moghaddam M, Ansari R, Sotoudeh M, Puolakkainen P, Kokkola A, Malekzadeh R, Knuutila S. Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing. J Mol Diagn 2016; 18:471-9. [PMID: 27155048 DOI: 10.1016/j.jmoldx.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 12/13/2022] Open
Abstract
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. One to five genes were mutated in 75% of cases. TP53, KRAS, FBXW7, and SMAD4 were the top mutated genes, consistent with previous studies. Of samples with mutations, 54% presented concomitant mutations in different genes. Phosphatidylinositol 3-kinase/mitogen-activated protein kinase pathway genes were mutated in 70% of samples, with 58% having alterations in KRAS, NRAS, or BRAF. Because mutations in these genes can compromise the efficacy of epidermal growth factor receptor blockade in CRC patients, identifying mutations that confer resistance to some targeted treatments may be useful to guide therapeutic decisions. In conclusion, the data presented herein show that NGS procedures on stool DNA represent a promising tool to detect genetic mutations that could be used in the future for diagnosis, monitoring, or treating CRC.
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Affiliation(s)
- Gemma Armengol
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Autonomous University of Barcelona, Barcelona, Spain
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Ansari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Pauli Puolakkainen
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Arto Kokkola
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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25
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Froyen G, Broekmans A, Hillen F, Pat K, Achten R, Mebis J, Rummens JL, Willemse J, Maes B. Validation and Application of a Custom-Designed Targeted Next-Generation Sequencing Panel for the Diagnostic Mutational Profiling of Solid Tumors. PLoS One 2016; 11:e0154038. [PMID: 27101000 PMCID: PMC4839685 DOI: 10.1371/journal.pone.0154038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 01/15/2023] Open
Abstract
The inevitable switch from standard molecular methods to next-generation sequencing for the molecular profiling of tumors is challenging for most diagnostic laboratories. However, fixed validation criteria for diagnostic accreditation are not in place because of the great variability in methods and aims. Here, we describe the validation of a custom panel of hotspots in 24 genes for the detection of somatic mutations in non-small cell lung carcinoma, colorectal carcinoma and malignant melanoma starting from FFPE sections, using 14, 36 and 5 cases, respectively. The targeted hotspots were selected for their present or future clinical relevance in solid tumor types. The target regions were enriched with the TruSeq approach starting from limited amounts of DNA. Cost effective sequencing of 12 pooled libraries was done using a micro flow cell on the MiSeq and subsequent data analysis with MiSeqReporter and VariantStudio. The entire workflow was diagnostically validated showing a robust performance with maximal sensitivity and specificity using as thresholds a variant allele frequency >5% and a minimal amplicon coverage of 300. We implemented this method through the analysis of 150 routine diagnostic samples and identified clinically relevant mutations in 16 genes including KRAS (32%), TP53 (32%), BRAF (12%), APC (11%), EGFR (8%) and NRAS (5%). Importantly, the highest success rate was obtained when using also the low quality DNA samples. In conclusion, we provide a workflow for the validation of targeted NGS by a custom-designed pan-solid tumor panel in a molecular diagnostic lab and demonstrate its robustness in a clinical setting.
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Affiliation(s)
- Guy Froyen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- * E-mail:
| | - An Broekmans
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Femke Hillen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Karin Pat
- Department of Pneumology, Jessa Hospital, Hasselt, Belgium
| | - Ruth Achten
- Department of Pathology, Jessa Hospital, Hasselt, Belgium
| | - Jeroen Mebis
- Department of Medical Oncology, Jessa Hospital, Hasselt, Belgium
| | - Jean-Luc Rummens
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Johan Willemse
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department of Clinical Biology, AZ Turnhout, Turnhout, Belgium
| | - Brigitte Maes
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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Houghton J, Hadd AG, Zeigler R, Haynes BC, Latham GJ. Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies. J Vis Exp 2016:e53836. [PMID: 27166994 PMCID: PMC4941914 DOI: 10.3791/53836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
All next-generation sequencing (NGS) procedures include assays performed at the laboratory bench ("wet bench") and data analyses conducted using bioinformatics pipelines ("dry bench"). Both elements are essential to produce accurate and reliable results, which are particularly critical for clinical laboratories. Targeted NGS technologies have increasingly found favor in oncology applications to help advance precision medicine objectives, yet the methods often involve disconnected and variable wet and dry bench workflows and uncoordinated reagent sets. In this report, we describe a method for sequencing challenging cancer specimens with a 21-gene panel as an example of a comprehensive targeted NGS system. The system integrates functional DNA quantification and qualification, single-tube multiplexed PCR enrichment, and library purification and normalization using analytically-verified, single-source reagents with a standalone bioinformatics suite. As a result, accurate variant calls from low-quality and low-quantity formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration (FNA) tumor biopsies can be achieved. The method can routinely assess cancer-associated variants from an input of 400 amplifiable DNA copies, and is modular in design to accommodate new gene content. Two different types of analytically-defined controls provide quality assurance and help safeguard call accuracy with clinically-relevant samples. A flexible "tag" PCR step embeds platform-specific adaptors and index codes to allow sample barcoding and compatibility with common benchtop NGS instruments. Importantly, the protocol is streamlined and can produce 24 sequence-ready libraries in a single day. Finally, the approach links wet and dry bench processes by incorporating pre-analytical sample quality control results directly into the variant calling algorithms to improve mutation detection accuracy and differentiate false-negative and indeterminate calls. This targeted NGS method uses advances in both wetware and software to achieve high-depth, multiplexed sequencing and sensitive analysis of heterogeneous cancer samples for diagnostic applications.
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27
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Asao T, Fujiwara Y, Sunami K, Kitahara S, Goto Y, Kanda S, Horinouchi H, Nokihara H, Yamamoto N, Ichikawa H, Kohno T, Tsuta K, Watanabe SI, Takahashi K, Ohe Y. Medical treatment involving investigational drugs and genetic profile of thymic carcinoma. Lung Cancer 2016; 93:77-81. [DOI: 10.1016/j.lungcan.2016.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/08/2015] [Accepted: 01/06/2016] [Indexed: 11/28/2022]
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Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform. Int J Mol Sci 2015; 16:28765-82. [PMID: 26633390 PMCID: PMC4691076 DOI: 10.3390/ijms161226129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/18/2015] [Accepted: 11/24/2015] [Indexed: 01/11/2023] Open
Abstract
Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.
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Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST). BMC Genomics 2015; 16:892. [PMID: 26531060 PMCID: PMC4630927 DOI: 10.1186/s12864-015-1982-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/04/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) has significantly impaired this process in the field of solid tumors. To evaluate if data generated from FFPE material can be reliably produced and potentially used in routine clinical settings, we performed whole exome sequencing (WES) from tumor samples of Gastrointestinal stromal tumors (GIST), either extracted FF or FFPE, and from matched normal DNA. METHODS We performed whole exome enrichment and sequencing at 100bp in paired end on four GIST samples, either from FFPE or fresh-frozen tissue, and from matched normal DNA. RESULTS The integrity of DNA extracted from FFPE was evaluated by a modified RAPD PCR method, thus identifying high quality (HQ) and low quality (LQ) FFPE. DNA library production and exome capture was feasible for both classes of FFPE, despite the smaller yield and insert size of LQ-FFPE. WES produced data of equal quality from FF and FFPE, while only HQ-FFPE yielded an amount of data comparable to FF samples. Bioinformatic analysis showed that the percentage of variants called both in FF and FFPE samples was very high in HQ-FFPE, reaching 94-96 % of the total number of called variants. Classification of somatic variants by nucleotide substitution type showed that HQ-FFPE and FF had similar mutational profiles, while LQ-FFPE samples carried a much higher number of mutations than the FF counterpart, with a significant enrichment of C > T/G > A substitutions. Focusing on potential disease-related variants allowed the discovery of additional somatic variants in GIST samples, apart from the known oncogenic driver mutation, both from sequencing of FF and FFPE material. False positive and false negative calls were present almost exclusively in the analysis of FFPE of low quality. On the whole this study showed that WES is feasible also on FFPE specimens and that it is possible to easily select FFPE samples of high quality that yield sequencing results comparable to the FF counterpart. CONCLUSIONS WES on FFPE material may represent an important and innovative source for GIST research and for other solid tumors, amenable of possible application in clinical practice.
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Moens LNJ, Falk-Sörqvist E, Ljungström V, Mattsson J, Sundström M, La Fleur L, Mathot L, Micke P, Nilsson M, Botling J. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples. J Mol Diagn 2015; 17:729-39. [PMID: 26354930 DOI: 10.1016/j.jmoldx.2015.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/29/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.
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Affiliation(s)
- Lotte N J Moens
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Magnus Sundström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Linnéa La Fleur
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
| | - Johan Botling
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden.
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31
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Bartels S, Schipper E, Kreipe HH, Lehmann U. Comprehensive Molecular Profiling of Archival Bone Marrow Trephines Using a Commercially Available Leukemia Panel and Semiconductor-Based Targeted Resequencing. PLoS One 2015. [PMID: 26222071 PMCID: PMC4519100 DOI: 10.1371/journal.pone.0133930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Comprehensive mutation profiling becomes more and more important in hematopathology complementing morphological and immunohistochemical evaluation of fixed, decalcified and embedded bone marrow biopsies for diagnostic, prognostic and also predictive purposes. However, the number and the size of relevant genes leave conventional Sanger sequencing impracticable in terms of costs, required input DNA, and turnaround time. Since most published protocols and commercially available reagents for targeted resequencing of gene panels are established and validated for the analysis of fresh bone marrow aspirate or peripheral blood it remains to be proven whether the available technology can be transferred to the analysis of archival trephines. Therefore, the performance of the recently available Ion AmpliSeq AML Research panel (LifeTechnologies) was evaluated for the analysis of fragmented DNA extracted from archival bone marrow trephines. Taking fresh aspirate as gold standard all clinically relevant mutations (n = 17) as well as 25 well-annotated SNPs could be identified reliably with high quality in the corresponding archival trephines of the training set (n = 10). Pre-treatment of the extracted DNA with Uracil-DNA-Glycosylase reduced the number of low level artificial sequence variants by more than 60%, vastly reducing time required for proper evaluation of the sequencing results. Subsequently, randomly picked FFPE samples (n = 41) were analyzed to evaluate sequencing performance under routine conditions. Thereby all known mutations (n = 43) could be verified and 36 additional mutations in genes not yet covered by the routine work-up (e.g., TET2, ASXL1, DNMT3A), demonstrating the feasibility of this approach and the gain of diagnostically relevant information. The dramatically reduced amount of input DNA, the increase in sensitivity as well as calculated cost-effectiveness, low hands on , and turn-around-time, necessary for the analysis of 237 amplicons strongly argue for replacing Sanger sequencing by this semiconductor-based targeted resequencing approach.
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Affiliation(s)
- Stephan Bartels
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Elisa Schipper
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- * E-mail:
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Appenzeller S, Gilissen C, Rijntjes J, Tops BBJ, Kastner-van Raaij A, Hebeda KM, Nissen L, Dutilh BE, van Krieken JHJM, Groenen PJTA. Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing. Histopathology 2015; 67:843-58. [DOI: 10.1111/his.12714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/14/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Silke Appenzeller
- Center for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
- Core Unit Systems Medicine; University of Wuerzburg; Wuerzburg Germany
| | - Christian Gilissen
- Department of Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Jos Rijntjes
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Bastiaan B J Tops
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Konnie M Hebeda
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Loes Nissen
- Department of Gastroenterology and Hepatology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Bas E Dutilh
- Center for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - J Han J M van Krieken
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
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Di Paolo A, Polillo M, Lastella M, Bocci G, Del Re M, Danesi R. Methods: for studying pharmacogenetic profiles of combination chemotherapeutic drugs. Expert Opin Drug Metab Toxicol 2015; 11:1253-67. [PMID: 26037261 DOI: 10.1517/17425255.2015.1053460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Molecular and genetic analysis of tumors and individuals has led to patient-centered therapies, through the discovery and identification of genetic markers predictive of drug efficacy and tolerability. Present therapies often include a combination of synergic drugs, each of them directed against different targets. Therefore, the pharmacogenetic profiling of tumor masses and patients is becoming a challenge, and several questions may arise when planning a translational study. AREAS COVERED The review presents the different techniques used to stratify oncology patients and to tailor antineoplastic treatments according to individual pharmacogenetic profiling. The advantages of these methodologies are discussed as well as current limits. EXPERT OPINION Facing the rapid technological evolution for genetic analyses, the most pressing issues are the choice of appropriate strategies (i.e., from gene candidate up to next-generation sequencing) and the possibility to replicate study results for their final validation. It is likely that the latter will be the major obstacle in the future. However, the present landscape is opening up new possibilities, overcoming those hurdles that have limited result translation into clinical settings for years.
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Affiliation(s)
- Antonello Di Paolo
- University of Pisa, Department of Clinical and Experimental Medicine, Via Roma 55, 56126 Pisa , Italy +39 050 2218755 ; +39 050 2218758 ;
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Kotoula V, Lyberopoulou A, Papadopoulou K, Charalambous E, Alexopoulou Z, Gakou C, Lakis S, Tsolaki E, Lilakos K, Fountzilas G. Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA. PLoS One 2015; 10:e0128818. [PMID: 26039550 PMCID: PMC4454570 DOI: 10.1371/journal.pone.0128818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AIM Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. METHODS Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. RESULTS Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman's rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8-99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1-95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3-76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. CONCLUSIONS Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.
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Affiliation(s)
- Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- Department of Pathology, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- * E-mail:
| | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | | | - Chryssa Gakou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Konstantinos Lilakos
- Department of Haematology, “Laikon” General Hospital, University of Athens Medical School, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
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Bellevicine C, Vigliar E, Malapelle U, Carelli E, Fiorelli A, Vicidomini G, Cappabianca S, Santini M, Troncone G. Lung adenocarcinoma and its thyroid metastasis characterized on fine-needle aspirates by cytomorphology, immunocytochemistry, and next-generation sequencing. Diagn Cytopathol 2015; 43:585-9. [DOI: 10.1002/dc.23264] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/23/2014] [Accepted: 01/31/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Claudio Bellevicine
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - Elena Vigliar
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - Umberto Malapelle
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - Emanuele Carelli
- Thoracic Surgery Unit; Second University of Naples; Naples Italy
| | - Alfonso Fiorelli
- Thoracic Surgery Unit; Second University of Naples; Naples Italy
| | | | - Salvatore Cappabianca
- Department of Internal and Experimental Medicine; Magrassi-Lanzara, Institute of Radiology, Second University of Naples; Naples Italy
| | - Mario Santini
- Thoracic Surgery Unit; Second University of Naples; Naples Italy
| | - Giancarlo Troncone
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
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Jia S, Zhang L, Latham GJ. In reply. Oncologist 2015; 20:e12. [PMID: 25862746 DOI: 10.1634/theoncologist.2014-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Shidong Jia
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California, USA
| | - Liangxuan Zhang
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California, USA
| | - Gary J Latham
- Research and Technology Development, Asuragen Inc., Austin, Texas, USA
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Stenzinger A, Pfarr N, Penzel R, Wolf T, Schirmacher P, Endris V, Weichert W. Semiconductor-based sequencing of formalin-fixed, paraffin-embedded colorectal cancer samples. Oncologist 2015; 20:e10-1. [PMID: 25862747 DOI: 10.1634/theoncologist.2014-0280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
| | - Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Wolf
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; National Center for Tumor Diseases, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
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Ananda G, Mockus S, Lundquist M, Spotlow V, Simons A, Mitchell T, Stafford G, Philip V, Stearns T, Srivastava A, Barter M, Rowe L, Malcolm J, Bult C, Karuturi RKM, Rasmussen K, Hinerfeld D. Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors. Exp Mol Pathol 2015; 98:106-12. [PMID: 25562415 DOI: 10.1016/j.yexmp.2014.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/25/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND The continued development of targeted therapeutics for cancer treatment has required the concomitant development of more expansive methods for the molecular profiling of the patient's tumor. We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment. METHODS NGS libraries are generated from DNA extracted from formalin fixed paraffin embedded tumors. Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report. RESULTS The JAX-CTP™ detects actionable variants, in the form of single nucleotide variations and small insertions and deletions (≤50 bp) in 190 genes in specimens with a neoplastic cell content of ≥10%. The JAX-CTP™ is also validated for the detection of clinically actionable gene amplifications. CONCLUSIONS There is a lack of consensus in the molecular diagnostics field on the best method for the validation of NGS-based assays in oncology, thus the importance of communicating methods, as contained in this report. The growing number of targeted therapeutics and the complexity of the tumor genome necessitate continued development and refinement of advanced assays for tumor profiling to enable precision cancer treatment.
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Affiliation(s)
- Guruprasad Ananda
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Susan Mockus
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Micaela Lundquist
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Vanessa Spotlow
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Al Simons
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Talia Mitchell
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Grace Stafford
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Vivek Philip
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Timothy Stearns
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Anuj Srivastava
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Mary Barter
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Lucy Rowe
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | - Joan Malcolm
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, 600 Main St, Bar Harbor, ME 04609, USA
| | | | - Karen Rasmussen
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Douglas Hinerfeld
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA.
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Abstract
AIMS To demonstrate clinical application of a mesodissection platform that was developed to combine advantages of laser-based instrumentation with the speed/ease of manual dissection for automated dissection of tissue off standard glass slides. METHODS Genomic analysis for KRAS gene mutation was performed on formalin fixed paraffin embedded (FFPE) cancer patient tissue that was dissected using the mesodissection platform. Selected reaction monitoring proteomic analysis for quantitative Her2 protein expression was performed on FFPE patient tumour tissue dissected by a laser-based instrument and the MilliSect instrument. RESULTS Genomic analysis demonstrates highly confident detection of KRAS mutation specifically in lung cancer cells and not the surrounding benign, non-tumour tissue. Proteomic analysis demonstrates Her2 quantitative protein expression in breast cancer cells dissected manually, by laser-based instrumentation and by MilliSect instrumentation (mesodissection). CONCLUSIONS Slide-mounted tissue dissection is commonly performed using laser-based instruments or manually scraping tissue by scalpel. Here we demonstrate that the mesodissection platform as performed by the MilliSect instrument for tissue dissection is cost-effective; it functions comparably to laser-based dissection and which can be adopted into a clinical diagnostic workflow.
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Affiliation(s)
| | - Nils Adey
- AvanSci Bio, Salt Lake City, Utah, USA
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Malapelle U, Vigliar E, Sgariglia R, Bellevicine C, Colarossi L, Vitale D, Pallante P, Troncone G. Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients. J Clin Pathol 2014; 68:64-8. [PMID: 25378536 DOI: 10.1136/jclinpath-2014-202691] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AIMS To evaluate the accuracy, consumable cost and time around testing (TAT) of a next-generation sequencing (NGS) assay, the Ion Torrent AmpliSeq Colon and Lung Cancer Panel, as an alternative to Sanger sequencing to genotype KRAS, NRAS and BRAF in colorectal cancer patients. METHODS The Ion Torrent panel was first verified on cell lines and on control samples and then prospectively applied to routine specimens (n=114), with Sanger sequencing as reference. RESULTS The Ion Torrent panel detected mutant alleles at the 5% level on cell lines and correctly classified all control tissues. The Ion Torrent assay was successfully carried out on most (95.6%) routine diagnostic samples. Of these, 12 (11%) harboured mutations in the BRAF gene and 47 (43%) in either of the two RAS genes, in two cases with a low abundance of RAS mutant allele which was missed by Sanger sequencing. The mean TAT, from sample receipt to reporting, was 10.4 (Sanger) and 13.0 (Ion Torrent) working days. The consumable cost for genotyping KRAS, NRAS and BRAF was €196 (Sanger) and €187 (Ion Torrent). CONCLUSIONS Ion Torrent AmpliSeq Colon and Lung Cancer Panel sequencing is as robust as Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor (EGFR) therapy for metastatic colorectal cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Lorenzo Colarossi
- Mediterranean Institute of Oncology (IOM), Catania, Italy PhD Programme in Biotechnology and Clinical Medicine, Sapienza University, Rome, Italy
| | | | - Pierlorenzo Pallante
- CNR/IEOS, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
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Kunze K, Spieker T, Gamerdinger U, Nau K, Berger J, Dreyer T, Sindermann JR, Hoffmeier A, Gattenlöhner S, Bräuninger A. A recurrent activating PLCG1 mutation in cardiac angiosarcomas increases apoptosis resistance and invasiveness of endothelial cells. Cancer Res 2014; 74:6173-83. [PMID: 25252913 DOI: 10.1158/0008-5472.can-14-1162] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Primary cardiac angiosarcomas are rare tumors with unfavorable prognosis. Pathogenic driver mutations are largely unknown. We therefore analyzed a collection of cases for genomic aberrations using SNP arrays and targeted next-generation sequencing (tNGS) of oncogenes and tumor-suppressor genes. Recurrent gains of chromosome 1q and a small region of chromosome 4 encompassing KDR and KIT were identified by SNP array analysis. Repeatedly mutated genes identified by tNGS were KDR with different nonsynonymous mutations, MLL2 with different nonsense mutations, and PLCG1 with a recurrent nonsynonymous mutation (R707Q) in the highly conserved autoinhibitory SH2 domain in three of 10 cases. PLCγ1 is usually activated by Y783 phosphorylation and activates protein kinase C and Ca(2+)-dependent second messengers, with effects on cellular proliferation, migration, and invasiveness. Ectopic expression of the PLCγ1-R707Q mutant in endothelial cells revealed reduced PLCγ1-Y783 phosphorylation with concomitant increased c-RAF/MEK/ERK1/2 phosphorylation, increased IP3 amounts, and increased Ca(2+)-dependent calcineurin activation compared with ectopic expressed PLCγ1-wild-type. Furthermore, cofilin, whose activation is associated with actin skeleton reorganization, showed decreased phosphorylation, and thus activation after expression of PLCγ1-R707Q compared with PLCγ1-wild-type. At the cellular level, expression of PLCγ1-R707Q in endothelial cells had no influence on proliferation rate, but increased apoptosis resistance and migration and invasiveness in in vitro assays. Together, these findings indicate that the PLCγ1-R707Q mutation causes constitutive activation of PLCγ1 and may represent an alternative way of activation of KDR/PLCγ1 signaling besides KDR activation in angiosarcomas, with implications for VEGF/KDR targeted therapies.
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Affiliation(s)
- Kristin Kunze
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tilmann Spieker
- Institute for Pathology, St. Francis Hospital, Münster, Germany
| | - Ulrike Gamerdinger
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Kerstin Nau
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Johannes Berger
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Thomas Dreyer
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jürgen R Sindermann
- Department of Cardiothoracic Surgery, Division of Cardiac Surgery, University Hospital Münster, Münster, Germany
| | - Andreas Hoffmeier
- Department of Cardiothoracic Surgery, Division of Cardiac Surgery, University Hospital Münster, Münster, Germany
| | | | - Andreas Bräuninger
- Department of Pathology, Justus-Liebig-University Giessen, Giessen, Germany.
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