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Abstract
Next-generation sequencing (NGS) has been rapidly integrated into molecular pathology, dramatically increasing the breadth genomic of information available to oncologists and their patients. This review will explore the ways in which this new technology is currently applied to bolster care for patients with solid tumors and hematological malignancies, focusing on practices and guidelines for assessing the technical validity and clinical utility of DNA variants identified during clinical NGS oncology testing.
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Affiliation(s)
- Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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52
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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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53
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Jesinghaus M, Pfarr N, Endris V, Kloor M, Volckmar AL, Brandt R, Herpel E, Muckenhuber A, Lasitschka F, Schirmacher P, Penzel R, Weichert W, Stenzinger A. Genotyping of colorectal cancer for cancer precision medicine: Results from the IPH Center for Molecular Pathology. Genes Chromosomes Cancer 2016; 55:505-21. [PMID: 26917275 DOI: 10.1002/gcc.22352] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/02/2016] [Accepted: 02/05/2016] [Indexed: 12/19/2022] Open
Abstract
Cancer precision medicine has opened up new avenues for the treatment of colorectal cancer (CRC). To fully realize its potential, high-throughput sequencing platforms that allow genotyping beyond KRAS need to be implemented and require performance assessment. We comprehensively analyzed first-year data of 202 consecutive formalin-fixed paraffin embedded (FFPE) CRC samples for which prospective genotyping at our institution was requested. Deep targeted genotyping was done using a semiconductor-based sequencing platform and a self-designed panel of 30 CRC-related genes. Additionally, microsatellite status (MS) was determined. Ninety-seven percent of tumor samples were suitable for sequencing and in 88% MS could be assessed. The minimal drop-out rates of 6 and 25 cases, respectively were due to too low amounts or heavy degradation of DNA. Of 557 nonsynonymous mutations, 90 (16%) have not been described in COSMIC at the time of data query. Forty-three cases (22%) had double- or triple mutations affecting a single gene. Sixty-four percent had genetic alterations influencing oncological therapy. Eight percent of patients (MSI phenotype: 6%; mutated POLE: 2%) were potentially eligible for treatment with immune checkpoint inhibitors. Of 56% of KRASwt CRC that potentially qualified for anti-EGFR treatment, 30% presented with mutations in BRAF/NRAS. Mutated PIK3CA was detected in 21%. In conclusion, we here present real-life routine diagnostics data that not only demonstrate the robustness and feasibility of deep targeted sequencing and MS-analysis of FFPE CRC samples but also contribute to the understanding of CRC genetics. Most importantly, in more than half of the patients our approach enabled the selection of the best treatment currently available. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Moritz Jesinghaus
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany
| | - Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Matthias Kloor
- Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Member of the German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,National Center for Tumor Diseases-Heidelberg School of Oncology (NCT-HSO), Heidelberg, Germany
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54
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de Leng WWJ, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FAS, Koudijs MJ, Nijman I, Hinrichs JWJ, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MHG, Sleijfer S, Willems SM, Lolkema MP. Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material. PLoS One 2016; 11:e0149405. [PMID: 26919633 PMCID: PMC4769293 DOI: 10.1371/journal.pone.0149405] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5% concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detection of low-frequency variants. The reliability of mutation analysis could be further improved with manual inspection of sequence data. Conclusion Targeted NGS can be reliably implemented in cancer diagnostics using both FFPE and FF tissue when using appropriate analysis settings, even with low input DNA.
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Affiliation(s)
- Wendy W. J. de Leng
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Christa G. Gadellaa-van Hooijdonk
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Françoise A. S. Barendregt-Smouter
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marco J. Koudijs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Ies Nijman
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - John W. J. Hinrichs
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stef van Lieshout
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Robert D. Loberg
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, 91320–1799, United States of America
| | - Maja de Jonge
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Emile E. Voest
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Roel A. de Weger
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Neeltje Steeghs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Marlies H. G. Langenberg
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stefan Sleijfer
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Martijn P. Lolkema
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
- * E-mail:
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55
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Malapelle U, Pisapia P, Sgariglia R, Vigliar E, Biglietto M, Carlomagno C, Giuffrè G, Bellevicine C, Troncone G. Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases. J Clin Pathol 2016; 69:767-71. [PMID: 26797410 PMCID: PMC5036215 DOI: 10.1136/jclinpath-2015-203403] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/29/2015] [Indexed: 12/20/2022]
Abstract
AIMS The incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers. METHODS Following a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes. RESULTS A total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%). CONCLUSIONS In a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Chiara Carlomagno
- Department of Surgical and Clinical Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Giuffrè
- Department of "Patologia Umana dell'Adulto e dell'età evolutiva, G.Barresi", University of Messina, Messina, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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56
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Caiazza F, Elliott L, Fennelly D, Sheahan K, Doherty GA, Ryan EJ. Targeting EGFR in metastatic colorectal cancer beyond the limitations of KRAS status: alternative biomarkers and therapeutic strategies. Biomark Med 2016; 9:363-75. [PMID: 25808440 DOI: 10.2217/bmm.15.5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Patients with metastatic colorectal cancer have a very poor prognosis. Incorporation of targeted molecular therapies, such as the anti-EGFR receptor monoclonal antibodies cetuximab and panitumumab, into treatment regimens has improved outcomes for patients with wild-type RAS tumors. Yet, response rates remain low and overall survival times are short. Increased understanding of oncogenic signaling pathways within the tumor, and how these are regulated by the inflammatory tumor microenvironment, is a priority to facilitate the development of biomarkers to better guide the use of existing therapies and to develop new ones. Here, we review recent preclinical and clinical progress in the development of biomarkers for predicting response to anti-EGFR therapy in metastatic colorectal cancer.
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Affiliation(s)
- Francesco Caiazza
- Centre for Colorectal Disease, St. Vincent's University Hospital, Elm Park, Dublin, Ireland
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57
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Gao J, Wu H, Wang L, Zhang H, Duan H, Lu J, Liang Z. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR. BMJ Open 2016; 6:e009532. [PMID: 26747035 PMCID: PMC4716245 DOI: 10.1136/bmjopen-2015-009532] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. SETTING Beijing, China. PARTICIPANTS 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. METHODS RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. RESULTS 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. CONCLUSIONS The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes.
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Affiliation(s)
- Jie Gao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Li Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
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58
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Vigliar E, Malapelle U, de Luca C, Bellevicine C, Troncone G. Challenges and opportunities of next-generation sequencing: a cytopathologist's perspective. Cytopathology 2015; 26:271-83. [DOI: 10.1111/cyt.12265] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 01/14/2023]
Affiliation(s)
- E. Vigliar
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - U. Malapelle
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - C. de Luca
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - C. Bellevicine
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - G. Troncone
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
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Butler KS, Young MYL, Li Z, Elespuru RK, Wood SC. Performance characteristics of the AmpliSeq Cancer Hotspot panel v2 in combination with the Ion Torrent Next Generation Sequencing Personal Genome Machine. Regul Toxicol Pharmacol 2015; 74:178-86. [PMID: 26387931 DOI: 10.1016/j.yrtph.2015.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022]
Abstract
Next-Generation Sequencing is a rapidly advancing technology that has research and clinical applications. For many cancers, it is important to know the precise mutation(s) present, as specific mutations could indicate or contra-indicate certain treatments as well as be indicative of prognosis. Using the Ion Torrent Personal Genome Machine and the AmpliSeq Cancer Hotspot panel v2, we sequenced two pancreatic cancer cell lines, BxPC-3 and HPAF-II, alone or in mixtures, to determine the error rate, sensitivity, and reproducibility of this system. The system resulted in coverage averaging 2000× across the various amplicons and was able to reliably and reproducibly identify mutations present at a rate of 5%. Identification of mutations present at a lower rate was possible by altering the parameters by which calls were made, but with an increase in erroneous, low-level calls. The panel was able to identify known mutations in these cell lines that are present in the COSMIC database. In addition, other, novel mutations were also identified that may prove clinically useful. The system was assessed for systematic errors such as homopolymer effects, end of amplicon effects and patterns in NO CALL sequence. Overall, the system is adequate at identifying the known, targeted mutations in the panel.
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Affiliation(s)
- Kimberly S Butler
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Megan Y L Young
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Zhihua Li
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Drug Evaluation and Research, Office of Translational Sciences, Office of Clinical Pharmacology, Division of Applied Regulatory Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Rosalie K Elespuru
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States
| | - Steven C Wood
- U.S. Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry and Materials Science, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
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D’Haene N, Le Mercier M, De Nève N, Blanchard O, Delaunoy M, El Housni H, Dessars B, Heimann P, Remmelink M, Demetter P, Tejpar S, Salmon I. Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers. PLoS One 2015; 10:e0138245. [PMID: 26366557 PMCID: PMC4569137 DOI: 10.1371/journal.pone.0138245] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022] Open
Abstract
Objective Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation. Methods We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed. Results Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%. Conclusions Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.
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Affiliation(s)
- Nicky D’Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Mélanie Delaunoy
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Hakim El Housni
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Barbara Dessars
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Pierre Heimann
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Myriam Remmelink
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Pieter Demetter
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Sabine Tejpar
- Department of Oncology, University Hospital Leuven, Leuven, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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61
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Simbolo M, Mafficini A, Agostini M, Pedrazzani C, Bedin C, Urso ED, Nitti D, Turri G, Scardoni M, Fassan M, Scarpa A. Next-generation sequencing for genetic testing of familial colorectal cancer syndromes. Hered Cancer Clin Pract 2015; 13:18. [PMID: 26300997 PMCID: PMC4546256 DOI: 10.1186/s13053-015-0039-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/12/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genetic screening in families with high risk to develop colorectal cancer (CRC) prevents incurable disease and permits personalized therapeutic and follow-up strategies. The advancement of next-generation sequencing (NGS) technologies has revolutionized the throughput of DNA sequencing. METHODS A series of 16 probands for either familial adenomatous polyposis (FAP; 8 cases) or hereditary nonpolyposis colorectal cancer (HNPCC; 8 cases) were investigated for intragenic mutations in five CRC familial syndromes-associated genes (APC, MUTYH, MLH1, MSH2, MSH6) applying both a custom multigene Ion AmpliSeq NGS panel and conventional Sanger sequencing. RESULTS Fourteen pathogenic variants were detected in 13/16 FAP/HNPCC probands (81.3 %); one FAP proband presented two co-existing pathogenic variants, one in APC and one in MUTYH. Thirteen of these 14 pathogenic variants were detected by both NGS and Sanger, while one MSH2 mutation (L280FfsX3) was identified only by Sanger sequencing. This is due to a limitation of the NGS approach in resolving sequences close or within homopolymeric stretches of DNA. To evaluate the performance of our NGS custom panel we assessed its capability to resolve the DNA sequences corresponding to 2225 pathogenic variants reported in the COSMIC database for APC, MUTYH, MLH1, MSH2, MSH6. Our NGS custom panel resolves the sequences where 2108 (94.7 %) of these variants occur. The remaining 117 mutations reside inside or in close proximity to homopolymer stretches; of these 27 (1.2 %) are imprecisely identified by the software but can be resolved by visual inspection of the region, while the remaining 90 variants (4.0 %) are blind spots. In summary, our custom panel would miss 4 % (90/2225) of pathogenic variants that would need a small set of Sanger sequencing reactions to be solved. CONCLUSIONS The multiplex NGS approach has the advantage of analyzing multiple genes in multiple samples simultaneously, requiring only a reduced number of Sanger sequences to resolve homopolymeric DNA regions not adequately assessed by NGS. The implementation of NGS approaches in routine diagnostics of familial CRC is cost-effective and significantly reduces diagnostic turnaround times.
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Affiliation(s)
- Michele Simbolo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Marco Agostini
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy ; Nano Inspired Biomedicine, Institute of Pediatric Research, Città della Speranza, Padua, Italy
| | - Corrado Pedrazzani
- Department of Surgery, General Surgery A, University of Verona, Verona, Italy
| | - Chiara Bedin
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy ; Nano Inspired Biomedicine, Institute of Pediatric Research, Città della Speranza, Padua, Italy
| | - Emanuele D Urso
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Donato Nitti
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Giona Turri
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Maria Scardoni
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Fassan
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy ; ARC-Net Research Centre, Department of Pathology & Diagnostics, University of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy ; Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy ; ARC-Net Research Centre, Department of Pathology & Diagnostics, University of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Verona, Italy
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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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63
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Vigliar E, Malapelle U, Troncone G. Cytopathology meets basic science. Cancer Cytopathol 2015; 123:571-2. [PMID: 26194340 DOI: 10.1002/cncy.21578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elena Vigliar
- Pathology and a fellowship in Cytopathology, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Research Fellow of Molecular Pathology, University of Naples Federico II, Naples, Italy
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Malapelle U, De Stefano A, Carlomagno C, Bellevicine C, Troncone G. Next-generation sequencing in the genomic profiling of synchronous colonic carcinomas: comment on Li et al (2015). J Clin Pathol 2015; 68:946-7. [PMID: 26139632 DOI: 10.1136/jclinpath-2015-203205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/04/2022]
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Alfonso De Stefano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Chiara Carlomagno
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Feng H, Wang X, Zhang Z, Tang C, Ye H, Jones L, Lou F, Zhang D, Jiang S, Sun H, Dong H, Zhang G, Liu Z, Dong Z, Guo B, Yan H, Yan C, Wang L, Su Z, Li Y, Nandakumar V, Huang XF, Chen SY, Liu D. Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing. Cancer Inform 2015; 14:83-93. [PMID: 26244006 PMCID: PMC4489668 DOI: 10.4137/cin.s22941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 12/18/2022] Open
Abstract
Lung cancer remains the most prevalent malignancy and the primary cause of cancer-related deaths worldwide. Unique mutations patterns can be found in lung cancer subtypes, in individual cancers, or within a single tumor, and drugs that target these genetic mutations and signal transduction pathways are often beneficial to patients. In this study, we used the Ion Torrent AmpliSeq Cancer Panel to sequence 737 loci from 45 cancer-related genes and oncogenes to identify genetic mutations in 48 formalin-fixed, paraffin-embedded (FFPE) human lung cancer samples from Chinese patients. We found frequent mutations in EGFR, KRAS, PIK3CA, and TP53 genes. Moreover, we observed that a portion of the lung cancer samples harbored two or more mutations in these key genes. This study demonstrates the feasibility of using the Ion Torrent sequencing to efficiently identify genetic mutations in individual tumors for targeted lung cancer therapy.
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Affiliation(s)
- Hongxiang Feng
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Xiaowei Wang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Zhenrong Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | | | - Hua Ye
- San Valley Biotechnology Inc., Beijing, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Feng Lou
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - Hong Sun
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - Zhiyuan Liu
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - He Yan
- San Valley Biotechnology Inc., Beijing, China
| | - Chaowei Yan
- San Valley Biotechnology Inc., Beijing, China
| | - Lu Wang
- San Valley Biotechnology Inc., Beijing, China
| | - Ziyi Su
- San Valley Biotechnology Inc., Beijing, China
| | - Yangyang Li
- San Valley Biotechnology Inc., Beijing, China
| | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xue F Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Deruo Liu
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
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Malapelle U, Sgariglia R, De Stefano A, Bellevicine C, Vigliar E, de Biase D, Sepe R, Pallante P, Carlomagno C, Tallini G, Troncone G. KRAS mutant allele-specific imbalance (MASI) assessment in routine samples of patients with metastatic colorectal cancer. J Clin Pathol 2015; 68:265-9. [PMID: 25609577 DOI: 10.1136/jclinpath-2014-202761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AIMS Patients with colorectal cancer harbouring KRAS mutations do not respond to antiepidermal growth factor receptor (anti-EGFR) therapy. Community screening for KRAS mutation selects patients for treatment. When a KRAS mutation is identified by direct sequencing, mutant and wild type alleles are seen on the sequencing electropherograms. KRAS mutant allele-specific imbalance (MASI) occurs when the mutant allele peak is higher than the wild type one. The aims of this study were to verify the rate and tissue distribution of KRAS MASI as well as its clinical relevance. METHODS A total of 437 sequencing electropherograms showing KRAS exon 2 mutation was reviewed and in 30 cases next generation sequencing (NGS) was also carried out. Five primary tumours were extensively laser capture microdissected to investigated KRAS MASI tissue spatial distribution. KRAS MASI influence on the overall survival was evaluated in 58 patients. In vitro response to anti-EGFR therapy in relation to different G13D KRAS MASI status was also evaluated. RESULTS On the overall, KRAS MASI occurred in 58/436 cases (12.8%), being more frequently associated with G13D mutation (p=0.05) and having a heterogeneous tissue distribution. KRAS MASI detection by Sanger Sequencing and NGS showed 94% (28/30) concordance. The longer overall survival of KRAS MASI negative patients did not reach statistical significance (p=0.08). In cell line model G13D KRAS MASI conferred resistance to cetuximab treatment. CONCLUSIONS KRAS MASI is a significant event in colorectal cancer, specifically associated with G13D mutation, and featuring a heterogeneous spatial distribution, that may have a role to predict the response to EGFR inhibitors. The foreseen implementation of NGS in community KRAS testing may help to define KRAS MASI prognostic and predictive significance.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Alfonso De Stefano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoles, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario de Biase
- Department of Medicine (DIMES)-Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Romina Sepe
- 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
| | - 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
| | - Chiara Carlomagno
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoles, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES)-Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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