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Betge J, Kerr G, Miersch T, Leible S, Erdmann G, Galata CL, Zhan T, Gaiser T, Post S, Ebert MP, Horisberger K, Boutros M. Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples. PLoS One 2015; 10:e0127146. [PMID: 26010451 PMCID: PMC4444292 DOI: 10.1371/journal.pone.0127146] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA isolated from resection specimens from 17 patients with colorectal cancer liver metastases. From ten of these patients, paired fresh frozen and routinely processed FFPE tissue was available for comparative study. Sample quality of FFPE tissues was determined by the amount of amplifiable DNA using qPCR, sequencing libraries were evaluated using Bioanalyzer. Three bioinformatic pipelines were compared for analysis of amplicon sequencing data. Selected hot spot mutations were reviewed using Sanger sequencing. In the sequenced samples from 16 patients, 29 non-synonymous coding mutations were identified in eleven genes. Most frequent were mutations in TP53 (10), APC (7), PIK3CA (3) and KRAS (2). A high concordance of FFPE and paired frozen tissue samples was observed in ten matched samples, revealing 21 identical mutation calls and only two mutations differing. Comparison of these results with two other commonly used variant calling tools, however, showed high discrepancies. Hence, amplicon sequencing can potentially be used to identify hot spot mutations in colorectal cancer metastases in frozen and FFPE tissue. However, remarkable differences exist among results of different variant calling tools, which are not only related to DNA sample quality. Our study highlights the need for standardization and benchmarking of variant calling pipelines, which will be required for translational and clinical applications.
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Affiliation(s)
- Johannes Betge
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- * E-mail: ;
| | - Grainne Kerr
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Thilo Miersch
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Svenja Leible
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Gerrit Erdmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Christian L. Galata
- Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tianzuo Zhan
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Institue of Pathology, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stefan Post
- Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P. Ebert
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Karoline Horisberger
- Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- * E-mail: ;
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102
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Zhou H, Mody DR, Smith D, Lloyd MB, Kemppainen J, Houghton J, Wylie D, Szafranska-Schwarzbach AE, Takei H. FNA needle rinses preserved in Cytolyt are acceptable specimen type for mutation testing of thyroid nodules. J Am Soc Cytopathol 2015; 4:128-135. [PMID: 31051693 DOI: 10.1016/j.jasc.2015.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/03/2015] [Accepted: 01/05/2015] [Indexed: 06/09/2023]
Abstract
INTRODUCTION This study investigated the application of molecular testing to residual thyroid fine-needle aspiration material from needle rinses collected in Cytolyt. MATERIALS AND METHODS Two thyroid needle rinses from 135 patients were collected in Cytolyt during routine diagnostic workup in our institution. Molecular testing was performed to detect 14 genetic alterations in BRAF, K-, H-, N-RAS genes as well as RET/PTC1, RET/PTC3, and PAX8/PPARγ and verified by next generation sequencing and correlated with cytologic diagnoses. RESULTS Molecular testing revealed a total of 17 mutations across specimens with benign nodule (n = 5; HRAS, NRAS), Hürthle cell neoplasm (n = 2; BRAF, HRAS) and Papillary thyroid carcinoma (n = 10, 9 BRAF, 1 KRAS) cytology. No RNA gene rearrangements were detected. CONCLUSIONS Mutations and translocations associated with thyroid cancer can be detected in thyroid fine-needle aspiration needle rinses preserved in Cytolyt specimens collected during routine patient management, which are typically discarded when a diagnosis is attained.
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Affiliation(s)
- Haijun Zhou
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas
| | - Dina R Mody
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Debora Smith
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas
| | - Maura B Lloyd
- Asuragen Clinical Services Laboratory, Austin, Texas
| | | | | | - Dennis Wylie
- Asuragen Clinical Services Laboratory, Austin, Texas
| | | | - Hidehiro Takei
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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Heuckmann JM, Thomas RK. A new generation of cancer genome diagnostics for routine clinical use: overcoming the roadblocks to personalized cancer medicine. Ann Oncol 2015; 26:1830-1837. [PMID: 25899787 DOI: 10.1093/annonc/mdv184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/07/2015] [Indexed: 12/22/2022] Open
Abstract
The identification of 'druggable' kinase gene alterations has revolutionized cancer treatment in the last decade by providing new and successfully targetable drug targets. Thus, genotyping tumors for matching the right patients with the right drugs have become a clinical routine. Today, advances in sequencing technology and computational genome analyses enable the discovery of a constantly growing number of genome alterations relevant for clinical decision making. As a consequence, several technological approaches have emerged in order to deal with these rapidly increasing demands for clinical cancer genome analyses. Here, we describe challenges on the path to the broad introduction of diagnostic cancer genome analyses and the technologies that can be applied to overcome them. We define three generations of molecular diagnostics that are in clinical use. The latest generation of these approaches involves deep and thus, highly sensitive sequencing of all therapeutically relevant types of genome alterations-mutations, copy number alterations and rearrangements/fusions-in a single assay. Such approaches therefore have substantial advantages (less time and less tissue required) over PCR-based methods that typically have to be combined with fluorescence in situ hybridization for detection of gene amplifications and fusions. Since these new technologies work reliably on routine diagnostic formalin-fixed, paraffin-embedded specimens, they can help expedite the broad introduction of personalized cancer therapy into the clinic by providing comprehensive, sensitive and accurate cancer genome diagnoses in 'real-time'.
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Affiliation(s)
| | - R K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.
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Heydt C, Kumm N, Fassunke J, Künstlinger H, Ihle MA, Scheel A, Schildhaus HU, Haller F, Büttner R, Odenthal M, Wardelmann E, Merkelbach-Bruse S. Massively parallel sequencing fails to detect minor resistant subclones in tissue samples prior to tyrosine kinase inhibitor therapy. BMC Cancer 2015; 15:291. [PMID: 25886408 PMCID: PMC4404105 DOI: 10.1186/s12885-015-1311-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Personalised medicine and targeted therapy have revolutionised cancer treatment. However, most patients develop drug resistance and relapse after showing an initial treatment response. Two theories have been postulated; either secondary resistance mutations develop de novo during therapy by mutagenesis or they are present in minor subclones prior to therapy. In this study, these two theories were evaluated in gastrointestinal stromal tumours (GISTs) where most patients develop secondary resistance mutations in the KIT gene during therapy with tyrosine kinase inhibitors. METHODS We used a cohort of 33 formalin-fixed, paraffin embedded (FFPE) primary GISTs and their corresponding recurrent tumours with known mutational status. The primary tumours were analysed for the secondary mutations of the recurrences, which had been identified previously. The primary tumours were resected prior to tyrosine kinase inhibitor therapy. Three ultrasensitive, massively parallel sequencing approaches on the GS Junior (Roche, Mannheim, Germany) and the MiSeq(TM) (Illumina, San Diego, CA, USA) were applied. Additionally, nine fresh-frozen samples resected prior to therapy were analysed for the most common secondary resistance mutations. RESULTS With a sensitivity level of down to 0.02%, no pre-existing resistant subclones with secondary KIT mutations were detected in primary GISTs. The sensitivity level varied for individual secondary mutations and was limited by sequencing artefacts on both systems. Artificial T > C substitutions at the position of the exon 13 p.V654A mutation, in particular, led to a lower sensitivity, independent from the source of the material. Fresh-frozen samples showed the same range of artificially mutated allele frequencies as the FFPE material. CONCLUSIONS Although we achieved a sufficiently high level of sensitivity, neither in the primary FFPE nor in the fresh-frozen GISTs we were able to detect pre-existing resistant subclones of the corresponding known secondary resistance mutations of the recurrent tumours. This supports the theory that secondary KIT resistance mutations develop under treatment by "de novo" mutagenesis. Alternatively, the detection limit of two mutated clones in 10,000 wild-type clones might not have been high enough or heterogeneous tissue samples, per se, might not be suitable for the detection of very small subpopulations of mutated cells.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Niklas Kumm
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Andreas Scheel
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Margarete Odenthal
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude D17, 48149, Münster, Germany.
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
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105
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Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups. Oncotarget 2015; 5:2839-52. [PMID: 24867389 PMCID: PMC4058049 DOI: 10.18632/oncotarget.1943] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One-hundred-fifty-three biliary cancers, including 70 intrahepatic cholangiocarcinomas (ICC), 57 extrahepatic cholangiocarcinomas (ECC) and 26 gallbladder carcinomas (GBC) were assessed for mutations in 56 genes using multigene next-generation sequencing. Expression of EGFR and mTOR pathway genes was investigated by immunohistochemistry. At least one mutated gene was observed in 118/153 (77%) cancers. The genes most frequently involved were KRAS (28%), TP53 (18%), ARID1A (12%), IDH1/2 (9%), PBRM1 (9%), BAP1 (7%), and PIK3CA (7%). IDH1/2 (p=0.0005) and BAP1 (p=0.0097) mutations were characteristic of ICC, while KRAS (p=0.0019) and TP53 (p=0.0019) were more frequent in ECC and GBC. Multivariate analysis identified tumour stage and TP53 mutations as independent predictors of survival. Alterations in chromatin remodeling genes (ARID1A, BAP1, PBRM1, SMARCB1) were seen in 31% of cases. Potentially actionable mutations were seen in 104/153 (68%) cancers: i) KRAS/NRAS/BRAF mutations were found in 34% of cancers; ii) mTOR pathway activation was documented by immunohistochemistry in 51% of cases and by mutations in mTOR pathway genes in 19% of cancers; iii) TGF-ß/Smad signaling was altered in 10.5% cancers; iv) mutations in tyrosine kinase receptors were found in 9% cases. Our study identified molecular subgroups of cholangiocarcinomas that can be explored for specific drug targeting in clinical trials.
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106
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Li-Chang HH, Kasaian K, Ng Y, Lum A, Kong E, Lim H, Jones SJ, Huntsman DG, Schaeffer DF, Yip S. Retrospective review using targeted deep sequencing reveals mutational differences between gastroesophageal junction and gastric carcinomas. BMC Cancer 2015; 15:32. [PMID: 25656989 PMCID: PMC4322811 DOI: 10.1186/s12885-015-1021-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 01/14/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Adenocarcinomas of both the gastroesophageal junction and stomach are molecularly complex, but differ with respect to epidemiology, etiology and survival. There are few data directly comparing the frequencies of single nucleotide mutations in cancer-related genes between the two sites. Sequencing of targeted gene panels may be useful in uncovering multiple genomic aberrations using a single test. METHODS DNA from 92 gastroesophageal junction and 75 gastric adenocarcinoma resection specimens was extracted from formalin-fixed paraffin-embedded tissue. Targeted deep sequencing of 46 cancer-related genes was performed through emulsion PCR followed by semiconductor-based sequencing. Gastroesophageal junction and gastric carcinomas were contrasted with respect to mutational profiles, immunohistochemistry and in situ hybridization, as well as corresponding clinicopathologic data. RESULTS Gastroesophageal junction carcinomas were associated with younger age, more frequent intestinal-type histology, more frequent p53 overexpression, and worse disease-free survival on multivariable analysis. Among all cases, 145 mutations were detected in 31 genes. TP53 mutations were the most common abnormality detected, and were more common in gastroesophageal junction carcinomas (42% vs. 27%, p = 0.036). Mutations in the Wnt pathway components APC and CTNNB1 were more common among gastric carcinomas (16% vs. 3%, p = 0.006), and gastric carcinomas were more likely to have ≥3 driver mutations detected (11% vs. 2%, p = 0.044). Twenty percent of cases had potentially actionable mutations identified. R132H and R132C missense mutations in the IDH1 gene were observed, and are the first reported mutations of their kind in gastric carcinoma. CONCLUSIONS Panel sequencing of routine pathology material can yield mutational information on several driver genes, including some for which targeted therapies are available. Differing rates of mutations and clinicopathologic differences support a distinction between adenocarcinomas that arise in the gastroesophageal junction and those that arise in the stomach proper.
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Affiliation(s)
- Hector H Li-Chang
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.
| | - Katayoon Kasaian
- University of British Columbia, Vancouver, Canada.
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.
| | - Ying Ng
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Amy Lum
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Esther Kong
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Howard Lim
- University of British Columbia, Vancouver, Canada.
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada.
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.
| | - David G Huntsman
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - David F Schaeffer
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
| | - Stephen Yip
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
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107
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Tops BBJ, Normanno N, Kurth H, Amato E, Mafficini A, Rieber N, Le Corre D, Rachiglio AM, Reiman A, Sheils O, Noppen C, Lacroix L, Cree IA, Scarpa A, Ligtenberg MJL, Laurent-Puig P. Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium. BMC Cancer 2015; 15:26. [PMID: 25637035 PMCID: PMC4318366 DOI: 10.1186/s12885-015-1015-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 01/08/2015] [Indexed: 01/05/2023] Open
Abstract
Background The number of predictive biomarkers that will be necessary to assess in clinical practice will increase with the availability of drugs that target specific molecular alterations. Therefore, diagnostic laboratories are confronted with new challenges: costs, turn-around-time and the amount of material required for testing will increase with the number of tests performed on a sample. Our consortium of European clinical research laboratories set out to test if semi-conductor sequencing provides a solution for these challenges. Methods We designed a multiplex PCR targeting 87 hotspot regions in 22 genes that are of clinical interest for lung and/or colorectal cancer. The gene-panel was tested by 7 different labs in their own clinical setting using ion-semiconductor sequencing. Results We analyzed 155 samples containing 112 previously identified mutations in the KRAS, EGFR en BRAF genes. Only 1 sample failed analysis due to poor quality of the DNA. All other samples were correctly genotyped for the known mutations, even as low as 2%, but also revealed other mutations. Optimization of the primers used in the multiplex PCR resulted in a uniform coverage distribution over the amplicons that allows for efficient pooling of samples in a sequencing run. Conclusions We show that a semi-conductor based sequencing approach to stratify colon and lung cancer patients is feasible in a clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1015-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bastiaan B J Tops
- Department of Pathology, Radboud University Medical Centre (Radboudumc), PO box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, 80131, Naples, Italy. .,Pharmacogenomic Laboratory, CROM - Centro Ricerche Oncologiche di Mercogliano, Mercogliano, 83013, Avellino, Italy.
| | - Henriette Kurth
- VIOLLIER, Department of Genetics/Molecular Biology, Basle, Switzerland.
| | - Eliana Amato
- ARC-NET Miriam Cherubini Research Centre, University of Verona, Verona, Italy.
| | - Andrea Mafficini
- ARC-NET Miriam Cherubini Research Centre, University of Verona, Verona, Italy.
| | - Nora Rieber
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - Delphine Le Corre
- Paris Sorbonne Cité; INSERM UMR-S775, Bases moléculaires des la réponses aux xénobiotiques, Paris, France.
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale", IRCCS, 80131, Naples, Italy.
| | - Anne Reiman
- Department of Pathology, Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK.
| | - Orla Sheils
- Department of Histopathology, The University of Dublin, Trinity College, Dublin, Ireland.
| | - Christoph Noppen
- VIOLLIER, Department of Genetics/Molecular Biology, Basle, Switzerland.
| | - Ludovic Lacroix
- Department of Medical Biology and Pathology, Translational research Laboratory and Biobank (UMS3655 CNRS/US23 INSERM), INSERM Unit U981, Gustave Roussy, Villejuif, France.
| | - Ian A Cree
- Department of Pathology, Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK.
| | - Aldo Scarpa
- ARC-NET Miriam Cherubini Research Centre, University of Verona, Verona, Italy. .,Department of Pathology and Diagnostics, University of Verona, Verona, Italy.
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Centre (Radboudumc), PO box 9101, 6500 HB, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Centre (Radboudumc), PO box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Pierre Laurent-Puig
- Paris Sorbonne Cité; INSERM UMR-S775, Bases moléculaires des la réponses aux xénobiotiques, Paris, France.
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Pižem J, Velikonja M, Matjašič A, Jerše M, Glavač D. Pseudoangiomatous stromal hyperplasia with multinucleated stromal giant cells is neither exceptional in gynecomastia nor characteristic of neurofibromatosis type 1. Virchows Arch 2015; 466:465-72. [PMID: 25586494 DOI: 10.1007/s00428-014-1715-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/03/2014] [Accepted: 12/22/2014] [Indexed: 01/21/2023]
Abstract
Six cases of gynecomastia with pseudoangiomatous stromal hyperplasia (PASH) and multinucleated stromal giant cells (MSGC) associated with neurofibromatosis type 1 (NF1) have been reported, and finding MSGC within PASH in gynecomastia has been suggested as being a characteristic of NF1. The frequency of PASH with MSGC in gynecomastia and its specificity for NF1 have not, however, been systematically studied. A total of 337 gynecomastia specimens from 215 patients, aged from 8 to 78 years (median, 22 years) were reevaluated for the presence of PASH with MSGC. Breast tissue samples of 25 patients were analyzed for the presence of an NF1 gene mutation using next generation sequencing. Rare MSGC, usually in the background of PASH, were noted at least unilaterally in 27 (13 %) patients; and prominent MSGC, always in the background of PASH, were noted in 8 (4 %) patients. The NF1 gene was mutated in only 1 (an 8-year-old boy with known NF1 and prominent MSGC) of the 25 tested patients, including 6 patients with prominent MSGC and 19 patients with rare MSGC. MSGC, usually in the background of PASH, are not characteristic of NF1.
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Affiliation(s)
- Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia,
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Gerdes MJ, Sood A, Sevinsky C, Pris AD, Zavodszky MI, Ginty F. Emerging understanding of multiscale tumor heterogeneity. Front Oncol 2014; 4:366. [PMID: 25566504 PMCID: PMC4270176 DOI: 10.3389/fonc.2014.00366] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022] Open
Abstract
Cancer is a multifaceted disease characterized by heterogeneous genetic alterations and cellular metabolism, at the organ, tissue, and cellular level. Key features of cancer heterogeneity are summarized by 10 acquired capabilities, which govern malignant transformation and progression of invasive tumors. The relative contribution of these hallmark features to the disease process varies between cancers. At the DNA and cellular level, germ-line and somatic gene mutations are found across all cancer types, causing abnormal protein production, cell behavior, and growth. The tumor microenvironment and its individual components (immune cells, fibroblasts, collagen, and blood vessels) can also facilitate or restrict tumor growth and metastasis. Oncology research is currently in the midst of a tremendous surge of comprehension of these disease mechanisms. This will lead not only to novel drug targets but also to new challenges in drug discovery. Integrated, multi-omic, multiplexed technologies are essential tools in the quest to understand all of the various cellular changes involved in tumorigenesis. This review examines features of cancer heterogeneity and discusses how multiplexed technologies can facilitate a more comprehensive understanding of these features.
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Affiliation(s)
- Michael J. Gerdes
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Anup Sood
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Christopher Sevinsky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Andrew D. Pris
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Maria I. Zavodszky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Fiona Ginty
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
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Tsongalis GJ, Peterson JD, de Abreu FB, Tunkey CD, Gallagher TL, Strausbaugh LD, Wells WA, Amos CI. Routine use of the Ion Torrent AmpliSeq™ Cancer Hotspot Panel for identification of clinically actionable somatic mutations. Clin Chem Lab Med 2014; 52:707-14. [PMID: 24334431 DOI: 10.1515/cclm-2013-0883] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/23/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND Somatic mutation analysis is standard of practice for solid tumors in order to identify therapeutic sensitizing and resistance mutations. Our laboratory routinely performed standalone PCR-based methods for mutations in several genes. Rapid discovery and introduction of new therapeutics has demanded additional genomic information for adequate management of the cancer patient. We evaluated a next generation sequencing assay, the Ion Torrent AmpliSeq Cancer Hotspot Panelv2 (CHPv2), capable of identifying multiple somatic mutations in 50 genes in a single assay. METHODS Accuracy, precision, limit of detection, and specificity were evaluated using DNA from well-characterized cell lines, genetically engineered cell lines fixed and embedded in paraffin, and previously tested mutation positive or negative, formalin-fixed, paraffin-embedded (FFPE) tissues. Normal kidney, tonsil and colon FFPE tissues were used as controls. RESULTS Accuracy studies showed 100% concordance in each patient sample between previous PCR results and the corresponding variants identified using the Ion Torrent panel. Precision studies gave consistent results when libraries were prepared from the same original DNA and were run on multiple 316 chips. The limit of detection was determined to be 5% for single nucleotide variants (SNVs) and 20% for insertions and deletions (indels). Specificity studies using normal FFPE tissue previously tested by PCR methods were also 100%. CONCLUSIONS We have evaluated the performance of the AmpliSeq Cancer Panel Hotspotv2 and show that it is suitable for clinical testing. This next generation sequencing panel has allowed the laboratory to consolidate a broader range of molecular oncology testing to a single platform and single assay.
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Choudhary A, Mambo E, Sanford T, Boedigheimer M, Twomey B, Califano J, Hadd A, Oliner KS, Beaudenon S, Latham GJ, Adai AT. Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel. BMC Med Genomics 2014; 7:62. [PMID: 25395014 PMCID: PMC4241214 DOI: 10.1186/s12920-014-0062-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 10/22/2014] [Indexed: 12/21/2022] Open
Abstract
Background Improvements in both performance and cost for next-generation sequencing (NGS) have spurred its rapid adoption for clinical applications. We designed and optimized a pan-cancer target-enrichment panel for 51 well-established oncogenes and tumor suppressors, in conjunction with a bioinformatic pipeline informed by in-process controls and pre- and post-analytical quality control measures. Methods The evaluation of this workflow consisted of sequencing mixtures of intact DNA to establish analytical sensitivity and precision, utilization of heuristics to identify systematic artifacts, titration studies of intact and FFPE samples for input optimization, and incorporation of orthogonal sequencing strategies to increase both positive predictive value and variant detection. We also used 128 FFPE samples to assess clinical accuracy and incorporated the previously described quantitative functional index (QFI) for sample qualification as part of detailing complete system performance. Results We observed a concordance correlation coefficient of 0.99 between the observed versus expected percent variant at 250 ng input across 4 independent sequencing runs. A subset of the systematic variants were confirmed to be barely detectable on an independent sequencing platform (Wilcox signed-rank test p-value <10−16), and the incorporation of orthogonal sequencing strategies increased the harmonic mean of sensitivity and positive predictive value of mutation detection by 41%. In one cohort of FFPE tumor samples, coverage and inter-platform concordance were positively correlated with the QFI, emphasizing the need for pre-analytical sample quality control to reduce the risk of false positives and negatives. In a separate cohort of FFPE samples, the 51-gene panel achieved 78% sensitivity (95% CI = 56.3, 92.5) with 100% PPV (95% CI = 81.5, 100.0) based on known mutations at 7.9% median abundance. By sequencing specimens using an orthogonal NGS technology, sensitivity was improved to 87.0% (95% CI = 66.4,97.2) while maintaining PPV. Conclusions The results highlight the value of process integration in a comprehensive targeted NGS system, enabling both discovery and diagnostic applications, particularly when sequencing low-quality cancer specimens. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0062-0) contains supplementary material, which is available to authorized users.
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112
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Le Mercier M, D'Haene N, De Nève N, Blanchard O, Degand C, Rorive S, Salmon I. Next-generation sequencing improves the diagnosis of thyroid FNA specimens with indeterminate cytology. Histopathology 2014; 66:215-24. [PMID: 24834793 DOI: 10.1111/his.12461] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/14/2014] [Indexed: 01/21/2023]
Abstract
AIMS The assessment of thyroid nodules is a common clinical challenge. Fine-needle aspiration (FNA) is the standard pre-operative tool for thyroid nodule diagnosis. However, up to 30% of the samples are classified as indeterminate. This often leads to unnecessary surgery. In this study, we evaluated the added value of next-generation sequencing (NGS) for helping in the diagnosis of FNA samples. METHODS AND RESULTS We analysed retrospectively 34 indeterminate FNA samples for which surgical resection was performed. DNA was obtained from cell blocks or from stained smears and subjected to NGS to analyse mutations in 50 genes. Mutations in BRAF, NRAS, KRAS and PTEN, that are known to be involved in thyroid cancer biology, were detected in seven FNA samples. The presence of a mutation in these genes was a strong indicator of cancer because five (71%) of the mutation-positive FNA samples had a malignant diagnosis after surgery. Moreover, there was only an 8% cancer risk in nodules with an indeterminate cytological diagnosis but with a negative molecular test. CONCLUSION This study demonstrates that thyroid FNA can be analysed successfully by NGS. The detection of mutations known to be involved in thyroid cancer improves the sensitivity of thyroid FNA diagnosis.
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Affiliation(s)
- Marie Le Mercier
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
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113
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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: 65] [Impact Index Per Article: 6.5] [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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114
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Walsh K, Wallace WA. Molecular pathology in lung cancer: a guide to the techniques used in clinical practice. Histopathology 2014; 65:731-41. [PMID: 25130601 DOI: 10.1111/his.12505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology. The use of molecular pathology assays in clinical samples is largely under the control of the histopathologist; who is likely to be asked, as a minimum, to select tissue sections for molecular analysis and mark areas of H&E stained slides for macro or microdissection. Many histopathologists will also be involved in the sourcing and implementation of new assays. This review aims to provide a guide to some of the most commonly used molecular pathology methods - their advantages and their limitations.
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Affiliation(s)
- Kathy Walsh
- Pathology, Division of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
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115
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Andre F, Mardis E, Salm M, Soria JC, Siu LL, Swanton C. Prioritizing targets for precision cancer medicine. Ann Oncol 2014; 25:2295-2303. [PMID: 25344359 DOI: 10.1093/annonc/mdu478] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The implementation of cancer genomic testing into the clinical setting has brought major opportunities. However, as our understanding of cancer initiation, maintenance and progression improves through detailed cancer genomic studies, the challenges associated with driver identification and target classification in the clinical setting become clearer. Here, we review recent insights into cancer genomic testing in the clinical setting, and suggest a target classification approach that considers the levels of evidence supporting the prioritization of tumour drivers for therapeutic targeting in light of complex cancer clonal and sub-clonal structures and clinical successes and failures in the field. We argue that such classification approaches, together with transparent reporting of both positive and negative clinical data and continued research to identify the sub-clonal dynamics of driver events during the disease course, will facilitate inter-trial comparisons, optimize patient informed consent and provide a critically balanced evaluation of genomic testing in clinical practice.
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Affiliation(s)
- F Andre
- Department of Medical Oncology, INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - E Mardis
- The Genome Institute, Washington University School of Medicine, St Louis, USA
| | - M Salm
- Cancer Research UK London Research Institute, London, UK
| | - J-C Soria
- DITEP, Gustave Roussy Cancer Campus, Villejuif, France
| | - L L Siu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - C Swanton
- Cancer Research UK London Research Institute, London, UK; UCL Hospitals and Cancer Institute, Huntley Street, London, UK.
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116
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Hoogstraat M, Hinrichs JWJ, Besselink NJM, Radersma-van Loon JH, de Voijs CMA, Peeters T, Nijman IJ, de Weger RA, Voest EE, Willems SM, Cuppen E, Koudijs MJ. Simultaneous detection of clinically relevant mutations and amplifications for routine cancer pathology. J Mol Diagn 2014; 17:10-8. [PMID: 25445215 DOI: 10.1016/j.jmoldx.2014.09.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 08/21/2014] [Accepted: 09/11/2014] [Indexed: 12/28/2022] Open
Abstract
In routine cancer molecular pathology, various independent experiments are required to determine mutation and amplification status of clinically relevant genes. Most of these tests are designed to identify a limited number of genetic aberrations, most likely in a given tumor type. We present a modified version of a multiplexed PCR and IonTorrent-based sequencing approach that can replace a large number of existing assays. The test allows for the simultaneous detection of point mutations and gene amplifications in 40 genes, including known hotspot regions in oncogenes (KRAS, BRAF), inactivating mutations in tumor suppressors (TP53, PTEN), and oncogene amplifications (ERBB2, EGFR). All point mutations were confirmed using certified diagnostic assays, and a sensitivity and specificity of 100% (95% CI, 0.875-1.0) and 99% (95% CI, 0.960-0.999), respectively, were determined for amplifications in FFPE material. Implementation of a single assay to effectively detect mutations and amplifications in clinically relevant genes not only improves the efficiency of the workflow within diagnostic laboratories but also increases the chance of detecting (rare) actionable variants for a given tumor type that are typically missed in routine pathology. The ability to obtain comprehensive and rapid mutational overviews is key for improving the efficiency of cancer patient care through tailoring treatments based on the genetic characteristics of individual tumors.
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Affiliation(s)
- Marlous Hoogstraat
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan Utrecht, Utrecht, the Netherlands; Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - John W J Hinrichs
- Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Nicolle J M Besselink
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan Utrecht, Utrecht, the Netherlands; Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Joyce H Radersma-van Loon
- Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Carmen M A de Voijs
- Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Ton Peeters
- Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Isaac J Nijman
- Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Roel A de Weger
- Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Emile E Voest
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan Utrecht, Utrecht, the Netherlands; Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands; Department of Pathology, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands.
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg Utrecht, Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Marco J Koudijs
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan Utrecht, Utrecht, the Netherlands; Netherlands Center for Personalized Cancer Treatment, Universiteitsweg Utrecht, Utrecht, the Netherlands
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Bohers E, Mareschal S, Bertrand P, Viailly PJ, Dubois S, Maingonnat C, Ruminy P, Tilly H, Jardin F. Activating somatic mutations in diffuse large B-cell lymphomas: lessons from next generation sequencing and key elements in the precision medicine era. Leuk Lymphoma 2014; 56:1213-22. [DOI: 10.3109/10428194.2014.941836] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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118
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Hansen AR, Bedard PL. Clinical application of high-throughput genomic technologies for treatment selection in breast cancer. Breast Cancer Res 2014; 15:R97. [PMID: 24135425 PMCID: PMC3979162 DOI: 10.1186/bcr3558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Large-scale collaborative initiatives using next-generation DNA sequencing and other high-throughput technologies have begun to characterize the genomic landscape of breast cancer. These landmark studies have identified infrequent driver mutations that are potential targets for therapeutic intervention with approved or investigational drug treatments, among other important discoveries. Recently, many institutions have launched molecular screening programs that apply high-throughput genomic technologies to patients with advanced solid malignancies, including breast cancer, to inform clinical decision-making. This article provides an overview of the recent molecular insights in breast cancer, including potentially actionable somatic alterations, the technological platforms currently available in a clinical diagnostics setting to detect these alterations, and ongoing institutional or regional molecular screening programs in advanced breast cancer.
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119
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Yip L. Molecular markers for thyroid cancer diagnosis, prognosis, and targeted therapy. J Surg Oncol 2014; 111:43-50. [PMID: 25155423 DOI: 10.1002/jso.23768] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022]
Abstract
Molecular markers including gene expression profiles, somatic gene alterations, and circulating peripheral markers have augmented diagnostic, prognostic, and therapeutic options for thyroid cancer patients.
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Affiliation(s)
- Linwah Yip
- Division of Endocrine Surgery and Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
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120
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Mafficini A, Amato E, Fassan M, Simbolo M, Antonello D, Vicentini C, Scardoni M, Bersani S, Gottardi M, Rusev B, Malpeli G, Corbo V, Barbi S, Sikora KO, Lawlor RT, Tortora G, Scarpa A. Reporting tumor molecular heterogeneity in histopathological diagnosis. PLoS One 2014; 9:e104979. [PMID: 25127237 PMCID: PMC4134249 DOI: 10.1371/journal.pone.0104979] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/14/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Detection of molecular tumor heterogeneity has become of paramount importance with the advent of targeted therapies. Analysis for detection should be comprehensive, timely and based on routinely available tumor samples. AIM To evaluate the diagnostic potential of targeted multigene next-generation sequencing (TM-NGS) in characterizing gastrointestinal cancer molecular heterogeneity. METHODS 35 gastrointestinal tract tumors, five of each intestinal type gastric carcinomas, pancreatic ductal adenocarcinomas, pancreatic intraductal papillary mucinous neoplasms, ampulla of Vater carcinomas, hepatocellular carcinomas, cholangiocarcinomas, pancreatic solid pseudopapillary tumors were assessed for mutations in 46 cancer-associated genes, using Ion Torrent semiconductor-based TM-NGS. One ampulla of Vater carcinoma cell line and one hepatic carcinosarcoma served to assess assay sensitivity. TP53, PIK3CA, KRAS, and BRAF mutations were validated by conventional Sanger sequencing. RESULTS TM-NGS yielded overlapping results on matched fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissues, with a mutation detection limit of 1% for fresh-frozen high molecular weight DNA and 2% for FFPE partially degraded DNA. At least one somatic mutation was observed in all tumors tested; multiple alterations were detected in 20/35 (57%) tumors. Seven cancers displayed significant differences in allelic frequencies for distinct mutations, indicating the presence of intratumor molecular heterogeneity; this was confirmed on selected samples by immunohistochemistry of p53 and Smad4, showing concordance with mutational analysis. CONCLUSIONS TM-NGS is able to detect and quantitate multiple gene alterations from limited amounts of DNA, moving one step closer to a next-generation histopathologic diagnosis that integrates morphologic, immunophenotypic, and multigene mutational analysis on routinely processed tissues, essential for personalized cancer therapy.
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Affiliation(s)
- Andrea Mafficini
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Eliana Amato
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Fassan
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Simbolo
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Davide Antonello
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Maria Scardoni
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Bersani
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Marisa Gottardi
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Giorgio Malpeli
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
- Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Stefano Barbi
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Katarzyna O. Sikora
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T. Lawlor
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Giampaolo Tortora
- Department of Medicine, Oncology Unit, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Applied Research on Cancer Network (ARC-NET) and Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
- * E-mail:
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121
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Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
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Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
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Heydt C, Fassunke J, Künstlinger H, Ihle MA, König K, Heukamp LC, Schildhaus HU, Odenthal M, Büttner R, Merkelbach-Bruse S. Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics. PLoS One 2014; 9:e104566. [PMID: 25105902 PMCID: PMC4126727 DOI: 10.1371/journal.pone.0104566] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022] Open
Abstract
Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
- * E-mail:
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Katharina König
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | | | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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Fisher KE, Cohen C, Siddiqui MT, Palma JF, Lipford EH, Longshore JW. Accurate detection of BRAF p.V600E mutations in challenging melanoma specimens requires stringent immunohistochemistry scoring criteria or sensitive molecular assays. Hum Pathol 2014; 45:2281-93. [PMID: 25228337 DOI: 10.1016/j.humpath.2014.07.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
Abstract
Malignant melanoma patients require BRAF mutation testing prior to initiating BRAF inhibitor therapy. Molecular testing remains the diagnostic gold standard, but recent work suggests that BRAF immunohistochemistry (IHC) confers comparable results. Sample attributes and scoring criteria that may affect BRAF IHC interpretation, however, are poorly defined. We investigated formalin-fixed, paraffin-embedded samples with variable challenging interpretative attributes: metastases, core needle biopsies, sample tissues less than 60 mm(2), samples with greater than 50% necrosis, and/or samples with greater than 10% melanin pigmentation. Three pathologists independently scored 122 BRAF V600E IHC-labeled melanoma samples for percentage (0%-100%) of staining intensity (0-3+). Interscorer BRAF IHC discrepancies were resolved by consensus review. Lenient (≥1+, >0%) and stringent (≥2+, ≥10%) IHC scoring criteria were compared to BRAF V600 mutation (cobas) results (n = 118). Specimens with greater than 10% melanin pigmentation and metastatic samples produced the majority of interobserver IHC and IHC/cobas scoring discrepancies. Consensus review using stringent scoring criteria decreased the number of discrepant results, yielded very good interobserver reproducibility, and improved specificity and positive predictive value for BRAF p.V600E detection. BRAF p.V600K mutations accounted for 57.1% of false-negative IHC results when stringent, consensus criteria scoring were used. The cobas test detected 75.0% (8/12) of BRAF IHC-negative BRAF p.V600K mutations confirmed by next-generation sequencing. Molecular BRAF testing is the preferred screening test for BRAF inhibitor therapy eligibility because of superior sensitivity in challenging interpretative melanoma specimens. However, BRAF V600E IHC has excellent specificity and positive predictive value when stringent, consensus scoring criteria are implemented. To decrease IHC scoring discrepancies, pathologists should interpret metastatic and pigmented samples with caution.
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Affiliation(s)
- Kevin E Fisher
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA.
| | - Cynthia Cohen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - John F Palma
- Roche Molecular Systems, Pleasanton, CA 94588, USA
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Hasemeier B, Geffers R, Bartels S, Schlegelberger B, Kreipe H, Lehmann U. Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology. Haematologica 2014; 98:e115-6. [PMID: 24006411 DOI: 10.3324/haematol.2013.091652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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125
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McCall CM, Mosier S, Thiess M, Debeljak M, Pallavajjala A, Beierl K, Deak KL, Datto MB, Gocke CD, Lin MT, Eshleman JR. False positives in multiplex PCR-based next-generation sequencing have unique signatures. J Mol Diagn 2014; 16:541-549. [PMID: 25017478 DOI: 10.1016/j.jmoldx.2014.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/02/2014] [Accepted: 06/16/2014] [Indexed: 01/11/2023] Open
Abstract
Next-generation sequencing shows great promise by allowing rapid mutational analysis of multiple genes in human cancers. Recently, we implemented the multiplex PCR-based Ion AmpliSeq Cancer Hotspot Panel (>200 amplicons in 50 genes) to evaluate EGFR, KRAS, and BRAF in lung and colorectal adenocarcinomas. In 10% of samples, automated analysis identified a novel G873R substitution mutation in EGFR. By examining reads individually, we found this mutation in >5% of reads in 50 of 291 samples and also found similar events in 18 additional amplicons. These apparent mutations are present only in short reads and within 10 bases of either end of the read. We therefore hypothesized that these were from panel primers promiscuously binding to nearly complementary sequences of nontargeted amplicons. Sequences around the mutations matched primer binding sites in the panel in 18 of 19 cases, thus likely corresponding to panel primers. Furthermore, because most primers did not show this effect, we demonstrated that next-generation sequencing may be used to better design multiplex PCR primers through iterative elimination of offending primers to minimize mispriming. Our results indicate the need for careful sequence analysis to avoid false-positive mutations that can arise in multiplex PCR panels. The AmpliSeq Cancer panel is a valuable tool for clinical diagnostics, provided awareness of potential artifacts.
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Affiliation(s)
- Chad M McCall
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stacy Mosier
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michele Thiess
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marija Debeljak
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Katie Beierl
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kristen L Deak
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Christopher D Gocke
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Ong M, Carreira S, Goodall J, Mateo J, Figueiredo I, Rodrigues DN, Perkins G, Seed G, Yap TA, Attard G, de Bono JS. Validation and utilisation of high-coverage next-generation sequencing to deliver the pharmacological audit trail. Br J Cancer 2014; 111:828-36. [PMID: 24983367 PMCID: PMC4150267 DOI: 10.1038/bjc.2014.350] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/14/2014] [Accepted: 06/02/2014] [Indexed: 12/22/2022] Open
Abstract
Background: Predictive biomarker development is a key challenge for novel cancer therapeutics. We explored the feasibility of next-generation sequencing (NGS) to validate exploratory genomic biomarkers that impact phase I trial selection. Methods: We prospectively enrolled 158 patients with advanced solid tumours referred for phase I clinical trials at the Royal Marsden Hospital (October 2012 to March 2013). After fresh and/or archived tumour tissue were obtained, 93 patients remained candidates for phase I trials. Results from tumour sequencing on the Illumina MiSeq were cross-validated in 27 out of 93 patients on the Ion Torrent Personal Genome Machine (IT-PGM) blinded to results. MiSeq validation with Sequenom MassARRAY OncoCarta 1.0 (Sequenom Inc., San Diego, CA, USA) was performed in a separate cohort. Results: We found 97% concordance of mutation calls by MiSeq and IT-PGM at a variant allele frequency ⩾13% and ⩾500 × depth coverage, and 91% concordance between MiSeq and Sequenom. Common ‘actionable' mutations involved deoxyribonucleic acid (DNA) repair (51%), RAS-RAF-MEK (35%), Wnt (26%), and PI3K-AKT-mTOR (24%) signalling. Out of 53, 29 (55%) patients participating in phase I trials were recommended based on identified actionable mutations. Conclusions: Targeted high-coverage NGS panels are a highly feasible single-centre technology well-suited to cross-platform validation, enrichment of trials with molecularly defined populations and hypothesis testing early in drug development.
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Affiliation(s)
- M Ong
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - S Carreira
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - J Goodall
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - J Mateo
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - I Figueiredo
- Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - D N Rodrigues
- Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - G Perkins
- Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - G Seed
- Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - T A Yap
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - G Attard
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
| | - J S de Bono
- 1] Cancer Biomarkers Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK [2] Drug Development Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT, UK
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Yeo ZX, Wong JCL, Rozen SG, Lee ASG. Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. BMC Genomics 2014; 15:516. [PMID: 24962530 PMCID: PMC4079958 DOI: 10.1186/1471-2164-15-516] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM’s reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. Results Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. Conclusions New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-516) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Steven G Rozen
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
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128
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Bai X, Zhang E, Ye H, Nandakumar V, Wang Z, Chen L, Tang C, Li J, Li H, Zhang W, Han W, Lou F, Zhang D, Sun H, Dong H, Zhang G, Liu Z, Dong Z, Guo B, Yan H, Yan C, Wang L, Su Z, Li Y, Jones L, Huang XF, Chen SY, Gao J. PIK3CA and TP53 gene mutations in human breast cancer tumors frequently detected by ion torrent DNA sequencing. PLoS One 2014; 9:e99306. [PMID: 24918944 PMCID: PMC4053449 DOI: 10.1371/journal.pone.0099306] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 05/13/2014] [Indexed: 12/19/2022] Open
Abstract
Breast cancer is the most common malignancy and the leading cause of cancer deaths in women worldwide. While specific genetic mutations have been linked to 5-10% of breast cancer cases, other environmental and epigenetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive breast cancer molecular profile is needed to develop more effective target therapies. Until recently, identifying genetic cancer mutations via personalized DNA sequencing was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 105 human breast cancer samples. The sequencing analysis revealed missense mutations in PIK3CA, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.
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Affiliation(s)
- Xusheng Bai
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Enke Zhang
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Hua Ye
- San Valley Biotechnology Incorporated, Beijing, China
| | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zhuo Wang
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Lihong Chen
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | | | - Jianhui Li
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Huijin Li
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Wei Zhang
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Wei Han
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
| | - Feng Lou
- San Valley Biotechnology Incorporated, Beijing, China
| | - Dandan Zhang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Hong Sun
- San Valley Biotechnology Incorporated, Beijing, China
| | - Haichao Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | | | - Zhiyuan Liu
- San Valley Biotechnology Incorporated, Beijing, China
| | - Zhishou Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | - Baishuai Guo
- San Valley Biotechnology Incorporated, Beijing, China
| | - He Yan
- San Valley Biotechnology Incorporated, Beijing, China
| | - Chaowei Yan
- San Valley Biotechnology Incorporated, Beijing, China
| | - Lu Wang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Ziyi Su
- San Valley Biotechnology Incorporated, Beijing, China
| | - Yangyang Li
- San Valley Biotechnology Incorporated, Beijing, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Xue F. Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (SYC); (JG)
| | - Jinglong Gao
- Central Laboratory, People’s Hospital of Shan Xi Province, Xian, China
- * E-mail: (SYC); (JG)
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Sehn JK, Abel HJ, Duncavage EJ. Copy number variants in clinical next-generation sequencing data can define the relationship between simultaneous tumors in an individual patient. Exp Mol Pathol 2014; 97:69-73. [PMID: 24886963 DOI: 10.1016/j.yexmp.2014.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 05/29/2014] [Indexed: 12/30/2022]
Abstract
Targeted next-generation sequencing (NGS) cancer panels have become a popular method for the identification of clinically predictive mutations in cancer. Such methods typically detect single nucleotide variants (SNVs) and small insertions/deletions (indels) in known cancer genes and can provide further information regarding diagnosis in challenging surgical pathology cases, as well as identify therapeutic targets and prognostically significant mutations. However, in addition to SNVs and indels, other mutation classes, including copy number variants (CNVs) and translocations, can be simultaneously detected from targeted NGS data. Here, as proof of methods, we present clinical data which demonstrate that targeted NGS panels can separate synchronous liver tumors based on CNV status, in the absence of distinct SNVs and indels. Such CNV-based analysis can be performed without additional cost using existing targeted cancer panel data and publically available software.
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Affiliation(s)
- Jennifer K Sehn
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Haley J Abel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric J Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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130
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Lin MT, Mosier SL, Thiess M, Beierl KF, Debeljak M, Tseng LH, Chen G, Yegnasubramanian S, Ho H, Cope L, Wheelan SJ, Gocke CD, Eshleman JR. Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am J Clin Pathol 2014; 141:856-66. [PMID: 24838331 DOI: 10.1309/ajcpmwgwgo34egod] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To validate next-generation sequencing (NGS) technology for clinical diagnosis and to determine appropriate read depth. METHODS We validated the KRAS, BRAF, and EGFR genes within the Ion AmpliSeq Cancer Hotspot Panel using the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA). RESULTS We developed a statistical model to determine the read depth needed for a given percent tumor cellularity and number of functional genomes. Bottlenecking can result from too few input genomes. By using 16 formalin-fixed, paraffin-embedded (FFPE) cancer-free specimens and 118 cancer specimens with known mutation status, we validated the six traditional analytic performance characteristics recommended by the Next-Generation Sequencing: Standardization of Clinical Testing Working Group. Baseline noise is consistent with spontaneous and FFPE-induced C:G→T:A deamination mutations. CONCLUSIONS Redundant bioinformatic pipelines are essential, since a single analysis pipeline gave false-negative and false-positive results. NGS is sufficiently robust for the clinical detection of gene mutations, with attention to potential artifacts.
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Affiliation(s)
- Ming-Tseh Lin
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Stacy L. Mosier
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Michele Thiess
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Katie F. Beierl
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Marija Debeljak
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Hui Tseng
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Guoli Chen
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Hao Ho
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Leslie Cope
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sarah J. Wheelan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D. Gocke
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R. Eshleman
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
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Abstract
In contemporary oncology practices there is an increasing emphasis on concurrent evaluation of multiple genomic alterations within the biological pathways driving tumorigenesis. At the foundation of this paradigm shift are several commercially available tumor panels using next-generation sequencing to develop a more complete molecular blueprint of the tumor. Ideally, these would be used to identify clinically actionable variants that can be matched with available molecularly targeted therapy, regardless of the tumor site or histology. Currently, there is little information available on the post-analytic processes unique to next-generation sequencing platforms used by the companies offering these tests. Additionally, evidence of clinical validity showing an association between the genetic markers curated in these tests with treatment response to approved molecularly targeted therapies is lacking across all solid-tumor types. To date, there is no published data of improved outcomes when using the commercially available tests to guide treatment decisions. The uniqueness of these tests from other genomic applications used to guide clinical treatment decisions lie in the sequencing platforms used to generate large amounts of genomic data, which have their own related issues regarding analytic and clinical validity, necessary precursors to the evaluation of clinical utility. The generation and interpretation of these data will require new evidentiary standards for establishing not only clinical utility, but also analytical and clinical validity for this emerging paradigm in oncology practice.
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Scott RJ, Fox SB, Desai J, Grieu F, Amanuel B, Garrett K, Harraway J, Cheetham G, Pattle N, Haddad A, Byron K, Rudzki B, Waring P, Iacopetta B. KRASmutation testing of metastatic colorectal cancer in Australia: Where are we at? Asia Pac J Clin Oncol 2014; 10:261-5. [DOI: 10.1111/ajco.12201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Rodney J. Scott
- Hunter Area Pathology Service; Newcastle New South Wales Australia
| | - Stephen B. Fox
- Peter MacCallum Cancer Centre; Melbourne Victoria Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre; Melbourne Victoria Australia
| | - Fabienne Grieu
- Department of Molecular Anatomic Pathology, PathWest QEII; Nedlands Western Australia Australia
| | - Benhur Amanuel
- Department of Molecular Anatomic Pathology, PathWest QEII; Nedlands Western Australia Australia
| | - Kerryn Garrett
- St John of God Pathology; Subiaco Western Australia Australia
| | - James Harraway
- Sullivan Nicolaides Pathology; Brisbane Queensland Australia
| | | | | | - Afaf Haddad
- Dorevitch Pathology; Melbourne Victoria Australia
| | - Keith Byron
- Healthscope Pathology; Clayton Victoria Australia
| | - Barney Rudzki
- Department of Pathology, University of Melbourne; Melbourne Victoria Australia
| | - Paul Waring
- Department of Pathology, University of Melbourne; Melbourne Victoria Australia
| | - Barry Iacopetta
- School of Surgery; University of Western Australia; Nedlands Western Australia Australia
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Cai X, Sheng J, Tang C, Nandakumar V, Ye H, Ji H, Tang H, Qin Y, Guan H, Lou F, Zhang D, Sun H, Dong H, Zhang G, Liu Z, Dong Z, Guo B, Yan H, Yan C, Wang L, Su Z, Li Y, Jones L, Huang XF, Chen SY, Wu T, Lin H. Frequent mutations in EGFR, KRAS and TP53 genes in human lung cancer tumors detected by ion torrent DNA sequencing. PLoS One 2014; 9:e95228. [PMID: 24760004 PMCID: PMC3997391 DOI: 10.1371/journal.pone.0095228] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 03/25/2014] [Indexed: 11/25/2022] Open
Abstract
Lung cancer is the most common malignancy and the leading cause of cancer deaths worldwide. While smoking is by far the leading cause of lung cancer, other environmental and genetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive lung cancer molecular profile is essential for developing more effective, tailored therapies. Until recently, personalized DNA sequencing to identify genetic mutations in cancer was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 76 human lung cancer samples. The sequencing analysis revealed missense mutations in KRAS, EGFR, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.
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Affiliation(s)
- Xin Cai
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jianhui Sheng
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | | | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, California, United States of America
| | - Hua Ye
- San Valley Biotechnology Incorporated, Beijing, China
| | - Hong Ji
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Haiying Tang
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yu Qin
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hongwei Guan
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Feng Lou
- San Valley Biotechnology Incorporated, Beijing, China
| | - Dandan Zhang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Hong Sun
- San Valley Biotechnology Incorporated, Beijing, China
| | - Haichao Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | | | - Zhiyuan Liu
- San Valley Biotechnology Incorporated, Beijing, China
| | - Zhishou Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | - Baishuai Guo
- San Valley Biotechnology Incorporated, Beijing, China
| | - He Yan
- San Valley Biotechnology Incorporated, Beijing, China
| | - Chaowei Yan
- San Valley Biotechnology Incorporated, Beijing, China
| | - Lu Wang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Ziyi Su
- San Valley Biotechnology Incorporated, Beijing, China
| | - Yangyang Li
- San Valley Biotechnology Incorporated, Beijing, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, California, United States of America
| | - Xue F. Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, California, United States of America
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, California, United States of America
| | - Taihua Wu
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hongli Lin
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol 2014; 4:78. [PMID: 24860780 PMCID: PMC4029014 DOI: 10.3389/fonc.2014.00078] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.
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Affiliation(s)
- Saumya Pant
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Russell Weiner
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Matthew J Marton
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
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Fang W, Radovich M, Zheng Y, Fu CY, Zhao P, Mao C, Zheng Y, Zheng S. 'Druggable' alterations detected by Ion Torrent in metastatic colorectal cancer patients. Oncol Lett 2014; 7:1761-1766. [PMID: 24932229 PMCID: PMC4049685 DOI: 10.3892/ol.2014.2047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/20/2014] [Indexed: 12/13/2022] Open
Abstract
The frequency and poor prognosis of patients with metastatic colorectal cancer (mCRC) emphasizes the requirement for improved biomarkers for use in the treatment and prognosis of mCRC. In the present study, somatic variants in exonic regions of key cancer genes were identified in mCRC patients. Formalin-fixed, paraffin-embedded tissues obtained by biopsy of the metastases of mCRC patients were collected, and the DNA was extracted and sequenced using the Ion Torrent Personal Genome Machine. For the targeted amplification of known cancer genes, the Ion AmpliSeq™ Cancer Panel, which is designed to detect 739 Catalogue of Somatic Mutations in Cancer (COSMIC) mutations in 604 loci from 46 oncogenes and tumor suppressor genes using as little as 10 ng of input DNA, was used. The sequencing results were then analyzed using the Ampliseq™ Variant Caller plug-in within the Ion Torrent Suite software. In addition, Ingenuity Pathway software was used to perform a pathway analysis. The Cox regression analysis was also conducted to investigate the potential correlation between alteration numbers and clinical factors, including response rate, disease-free survival and overall survival. Among 10 specimens, 65 genetic alterations were identified in 24 genes following the exclusion of germline mutations using the SNP database, whereby 41% of the alterations were also present in the COSMIC database. No clinical factors were found to significantly correlate with the alteration numbers in the patients by statistical analysis. However, pathway analysis identified ‘colorectal cancer metastasis signaling’ as the most commonly mutated canonical pathway. This analysis further revealed mutated genes in the Wnt, phosphoinositide 3-kinase (PI3K)/AKT and transforming growth factor (TGF)-β/SMAD signaling pathways. Notably, 11 genes, including the expected APC, BRAF, KRAS, PIK3CA and TP53 genes, were mutated in at least two samples. Notably, 90% (9/10) of mCRC patients harbored at least one ‘druggable’ alteration (range, 1–6 alterations) that has been linked to a clinical treatment option or is currently being investigated in clinical trials of novel targeted therapies. These results indicated that DNA sequencing of key oncogenes and tumor suppressors enables the identification of ‘druggable’ alterations for individual colorectal cancer patients.
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Affiliation(s)
- Weijia Fang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Milan Radovich
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yulong Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Cai-Yun Fu
- Laboratory of Proteomics and Molecular Enzymology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Peng Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Chengyu Mao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yi Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
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Gaykalova DA, Mambo E, Choudhary A, Houghton J, Buddavarapu K, Sanford T, Darden W, Adai A, Hadd A, Latham G, Danilova LV, Bishop J, Li RJ, Westra WH, Hennessey P, Koch WM, Ochs MF, Califano JA, Sun W. Novel insight into mutational landscape of head and neck squamous cell carcinoma. PLoS One 2014; 9:e93102. [PMID: 24667986 PMCID: PMC3965530 DOI: 10.1371/journal.pone.0093102] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/28/2014] [Indexed: 12/30/2022] Open
Abstract
Development of head and neck squamous cell carcinoma (HNSCC) is characterized by accumulation of mutations in several oncogenes and tumor suppressor genes. We have formerly described the mutation pattern of HNSCC and described NOTCH signaling pathway alterations. Given the complexity of the HNSCC, here we extend the previous study to understand the overall HNSCC mutation context and to discover additional genetic alterations. We performed high depth targeted exon sequencing of 51 highly actionable cancer-related genes with a high frequency of mutation across many cancer types, including head and neck. DNA from primary tumor tissues and matched normal tissues was analyzed for 37 HNSCC patients. We identified 26 non-synonymous or stop-gained mutations targeting 11 of 51 selected genes. These genes were mutated in 17 out of 37 (46%) studied HNSCC patients. Smokers harbored 3.2-fold more mutations than non-smokers. Importantly, TP53 was mutated in 30%, NOTCH1 in 8% and FGFR3 in 5% of HNSCC. HPV negative patients harbored 4-fold more TP53 mutations than HPV positive patients. These data confirm prior reports of the HNSCC mutational profile. Additionally, we detected mutations in two new genes, CEBPA and FES, which have not been previously reported in HNSCC. These data extend the spectrum of HNSCC mutations and define novel mutation targets in HNSCC carcinogenesis, especially for smokers and HNSCC without HPV infection.
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Affiliation(s)
- Daria A. Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | | | | | | | | | | | - Will Darden
- Asuragen Inc., Austin, Texas, United States of America
| | - Alex Adai
- Asuragen Inc., Austin, Texas, United States of America
| | - Andrew Hadd
- Asuragen Inc., Austin, Texas, United States of America
| | - Gary Latham
- Asuragen Inc., Austin, Texas, United States of America
| | - Ludmila V. Danilova
- Department of Oncology and Health Science Informatics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Justin Bishop
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Ryan J. Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - William H. Westra
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Patrick Hennessey
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wayne M. Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Michael F. Ochs
- Department of Oncology and Health Science Informatics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail: (WS); (JAC)
| | - Wenyue Sun
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- * E-mail: (WS); (JAC)
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Zhang L, Chen L, Sah S, Latham GJ, Patel R, Song Q, Koeppen H, Tam R, Schleifman E, Mashhedi H, Chalasani S, Fu L, Sumiyoshi T, Raja R, Forrest W, Hampton GM, Lackner MR, Hegde P, Jia S. Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing. Oncologist 2014; 19:336-43. [PMID: 24664487 DOI: 10.1634/theoncologist.2013-0180] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology. METHODS We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls. RESULTS Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA. CONCLUSION AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.
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Affiliation(s)
- Liangxuan Zhang
- Departments of Oncology Biomarker Development, Biostatistics, and Pathology, Genentech Inc., South San Francisco, California, USA; Technology Development, Asuragen Inc., Austin, Texas, USA
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Schleifman EB, Tam R, Patel R, Tsan A, Sumiyoshi T, Fu L, Desai R, Schoenbrunner N, Myers TW, Bauer K, Smith E, Raja R. Next generation MUT-MAP, a high-sensitivity high-throughput microfluidics chip-based mutation analysis panel. PLoS One 2014; 9:e90761. [PMID: 24658394 PMCID: PMC3962342 DOI: 10.1371/journal.pone.0090761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/03/2014] [Indexed: 11/19/2022] Open
Abstract
Molecular profiling of tumor tissue to detect alterations, such as oncogenic mutations, plays a vital role in determining treatment options in oncology. Hence, there is an increasing need for a robust and high-throughput technology to detect oncogenic hotspot mutations. Although commercial assays are available to detect genetic alterations in single genes, only a limited amount of tissue is often available from patients, requiring multiplexing to allow for simultaneous detection of mutations in many genes using low DNA input. Even though next-generation sequencing (NGS) platforms provide powerful tools for this purpose, they face challenges such as high cost, large DNA input requirement, complex data analysis, and long turnaround times, limiting their use in clinical settings. We report the development of the next generation mutation multi-analyte panel (MUT-MAP), a high-throughput microfluidic, panel for detecting 120 somatic mutations across eleven genes of therapeutic interest (AKT1, BRAF, EGFR, FGFR3, FLT3, HRAS, KIT, KRAS, MET, NRAS, and PIK3CA) using allele-specific PCR (AS-PCR) and Taqman technology. This mutation panel requires as little as 2 ng of high quality DNA from fresh frozen or 100 ng of DNA from formalin-fixed paraffin-embedded (FFPE) tissues. Mutation calls, including an automated data analysis process, have been implemented to run 88 samples per day. Validation of this platform using plasmids showed robust signal and low cross-reactivity in all of the newly added assays and mutation calls in cell line samples were found to be consistent with the Catalogue of Somatic Mutations in Cancer (COSMIC) database allowing for direct comparison of our platform to Sanger sequencing. High correlation with NGS when compared to the SuraSeq500 panel run on the Ion Torrent platform in a FFPE dilution experiment showed assay sensitivity down to 0.45%. This multiplexed mutation panel is a valuable tool for high-throughput biomarker discovery in personalized medicine and cancer drug development.
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Affiliation(s)
- Erica B. Schleifman
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rachel Tam
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rajesh Patel
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Alison Tsan
- Chemistry and Innovation Technology, Pleasanton, California, United States of America
| | - Teiko Sumiyoshi
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Ling Fu
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rupal Desai
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Nancy Schoenbrunner
- Chemistry and Innovation Technology, Pleasanton, California, United States of America
| | - Thomas W. Myers
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Keith Bauer
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Edward Smith
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Rajiv Raja
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
- * E-mail:
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140
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Ohori NP, Schoedel KE. Ancillary Studies in Thyroid Cytopathology. Surg Pathol Clin 2014; 7:47-60. [PMID: 26839268 DOI: 10.1016/j.path.2013.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent advances in thyroid imaging, clinical evaluation, cytopathology, surgical pathology, and molecular diagnostics have contributed toward greater understanding of thyroid nodules. In particular, the development of the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) has brought standardization to the field and the system dovetails well with the implementation of immunohistochemistry and molecular testing to diagnostic practice. Among the molecular strategies available, the application of the molecular panel of common genetic alterations can stratify indeterminate BSRTC diagnoses into low-risk and high-risk groups. The molecular panel markers have a high positive predictive value and therefore, the panel is considered to be a "rule-in" test. In contrast, the Afirma gene expression classifier by Veracyte Corporation is a test that has been reported to have a high negative predictive value, and therefore, considered to be a "rule-out" test. With further advances, refinements are expected to be made. In particular, the application of next-generation sequencing technology holds promise in bringing thyroid cytopathology to the next level.
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Affiliation(s)
- N Paul Ohori
- Department of Pathology, University of Pittsburgh Medical Center-Presbyterian, A610, 200 Lothrop Street, Pittsburgh, PA 15213, USA.
| | - Karen E Schoedel
- Department of Pathology, University of Pittsburgh Medical Center-Presbyterian, A610, 200 Lothrop Street, Pittsburgh, PA 15213, USA
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141
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Bourgon R, Lu S, Yan Y, Lackner MR, Wang W, Weigman V, Wang D, Guan Y, Ryner L, Koeppen H, Patel R, Hampton GM, Amler LC, Wang Y. High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing. Clin Cancer Res 2014; 20:2080-91. [PMID: 24573554 DOI: 10.1158/1078-0432.ccr-13-3114] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Tailoring cancer treatment to tumor molecular characteristics promises to make personalized medicine a reality. However, reliable genetic profiling of archived clinical specimens has been hindered by limited sensitivity and high false-positive rates. Here, we describe a novel methodology, MMP-seq, which enables sensitive and specific high-throughput, high-content genetic profiling in archived clinical samples. EXPERIMENTAL DESIGN We first validated the technical performance of MMP-seq in 66 cancer cell lines and a Latin square cross-dilution of known somatic mutations. We next characterized the performance of MMP-seq in 17 formalin-fixed paraffin-embedded (FFPE) clinical samples using matched fresh-frozen tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 patients with endometrial cancer. RESULTS We demonstrated that MMP-seq enabled rapid and simultaneous profiling of a panel of 88 cancer genes in 48 samples, and detected variants at frequencies as low as 0.4%. We identified DNA degradation and deamination as the main error sources and developed practical and robust strategies for mitigating these issues, and dramatically reduced the false-positive rate. Applying MMP-seq to a cohort of endometrial tumor samples identified extensive, potentially actionable alterations in the PI3K (phosphoinositide 3-kinase) and RAS pathways, including novel PIK3R1 hotspot mutations that may disrupt negative regulation of PIK3CA. CONCLUSIONS MMP-seq provides a robust solution for comprehensive, reliable, and high-throughput genetic profiling of clinical tumor samples, paving the way for the incorporation of genomic-based testing into clinical investigation and practice.
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Affiliation(s)
- Richard Bourgon
- Authors' Affiliations: Departments of Oncology Biomarker Development, Bioinformatics, Structural Biology, and Pathology, Genentech, Inc.; Fluidigm Inc., South San Francisco, California; and Expression Analysis, Durham, North Carolina
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A Multicenter Blinded Study Evaluating EGFR and KRAS Mutation Testing Methods in the Clinical Non–Small Cell Lung Cancer Setting—IFCT/ERMETIC2 Project Part 1. J Mol Diagn 2014; 16:45-55. [DOI: 10.1016/j.jmoldx.2013.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 07/04/2013] [Accepted: 07/30/2013] [Indexed: 11/22/2022] Open
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Kim HS, Sung JS, Yang SJ, Kwon NJ, Jin L, Kim ST, Park KH, Shin SW, Kim HK, Kang JH, Kim JO, Park JY, Choi JE, Yoon H, Park CK, Yang KS, Seo JS, Kim YH. Predictive efficacy of low burden EGFR mutation detected by next-generation sequencing on response to EGFR tyrosine kinase inhibitors in non-small-cell lung carcinoma. PLoS One 2013; 8:e81975. [PMID: 24376508 PMCID: PMC3869671 DOI: 10.1371/journal.pone.0081975] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/18/2013] [Indexed: 11/21/2022] Open
Abstract
Direct sequencing remains the most widely used method for the detection of epidermal growth factor receptor (EGFR) mutations in lung cancer; however, its relatively low sensitivity limits its clinical use. The objective of this study was to investigate the sensitivity of detecting an epidermal growth factor receptor (EGFR) mutation from peptide nucleic acid-locked nucleic acid polymerase chain reaction (PNA-LNA PCR) clamp and Ion Torrent Personal Genome Machine (PGM) techniques compared to that by direct sequencing. Furthermore, the predictive efficacy of EGFR mutations detected by PNA-LNA PCR clamp was evaluated. EGFR mutational status was assessed by direct sequencing, PNA-LNA PCR clamp, and Ion Torrent PGM in 57 patients with non-small cell lung cancer (NSCLC). We evaluated the predictive efficacy of PNA-LNA PCR clamp on the EGFR-TKI treatment in 36 patients with advanced NSCLC retrospectively. Compared to direct sequencing (16/57, 28.1%), PNA-LNA PCR clamp (27/57, 47.4%) and Ion Torrent PGM (26/57, 45.6%) detected more EGFR mutations. EGFR mutant patients had significantly longer progressive free survival (14.31 vs. 21.61 months, P = 0.003) than that of EGFR wild patients when tested with PNA-LNA PCR clamp. However, no difference in response rate to EGFR TKIs (75.0% vs. 82.4%, P = 0.195) or overall survival (34.39 vs. 44.10 months, P = 0.422) was observed between the EGFR mutations by direct sequencing or PNA-LNA PCR clamp. Our results demonstrate firstly that patients with EGFR mutations were detected more frequently by PNA-LNA PCR clamp and Ion Torrent PGM than those by direct sequencing. EGFR mutations detected by PNA-LNA PCR clamp may be as a predicative factor for EGFR TKI response in patients with NSCLC.
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Affiliation(s)
- Hye Sook Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Jae Sook Sung
- Cancer Research Institute, Korea University, Seoul, Korea
| | | | | | - LiHua Jin
- Cancer Research Institute, Korea University, Seoul, Korea
| | - Seung Tae Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Sang Won Shin
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Han Kyeom Kim
- Department of Pathology, College of Medicine, Korea University, Seoul, Korea
| | - Jin-Hyoung Kang
- Division of Medical Oncology, Seoul Saint Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jeong-Oh Kim
- Laboratory of Medical Oncology, Research Institutes of Medical Science, The Catholic University of Korea, Korea
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Korea
| | - HyoungKyu Yoon
- Division of Pulmonology, Department of Internal Medicine, Saint Mary's Hospital, College of Medicine, The Catholic University of Korea, Korea
| | - Chan Kwon Park
- Division of Pulmonology, Department of Internal Medicine, Saint Mary's Hospital, College of Medicine, The Catholic University of Korea, Korea
| | | | - Jeong-Sun Seo
- Macroge Inc., Seoul, Korea
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- * E-mail: (YHK); (J. Seo)
| | - Yeul Hong Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
- Cancer Research Institute, Korea University, Seoul, Korea
- * E-mail: (YHK); (J. Seo)
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144
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Yip L. Use of Molecular Markers for Cytologically Indeterminate Thyroid Nodules to Optimize Surgical Management. CURRENT SURGERY REPORTS 2013. [DOI: 10.1007/s40137-013-0035-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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145
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Hagemann IS, Cottrell CE, Lockwood CM. Design of targeted, capture-based, next generation sequencing tests for precision cancer therapy. Cancer Genet 2013; 206:420-31. [DOI: 10.1016/j.cancergen.2013.11.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 12/15/2022]
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146
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Molecular Diagnostic Profiling of Lung Cancer Specimens with a Semiconductor-Based Massive Parallel Sequencing Approach. J Mol Diagn 2013; 15:765-75. [DOI: 10.1016/j.jmoldx.2013.06.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/10/2013] [Accepted: 06/11/2013] [Indexed: 01/11/2023] Open
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147
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Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A, Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JM, Rubin MA, Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D, Yelensky R. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol 2013; 31:1023-31. [PMID: 24142049 PMCID: PMC5710001 DOI: 10.1038/nbt.2696] [Citation(s) in RCA: 1649] [Impact Index Per Article: 149.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/19/2013] [Indexed: 02/07/2023]
Abstract
As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. Here we describe a test based on massively parallel DNA sequencing to characterize base substitutions, short insertions and deletions (indels), copy number alterations and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens. We implemented a practical validation strategy with reference samples of pooled cell lines that model key determinants of accuracy, including mutant allele frequency, indel length and amplitude of copy change. Test sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%). We confirmed accuracy using 249 FFPE cancer specimens characterized by established assays. Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests.
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Affiliation(s)
| | | | - Geoff A Otto
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Kai Wang
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Jie He
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Jared White
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Peter An
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - James Sun
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Frank Juhn
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Kiel Iwanik
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Jamie Buell
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Emily White
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Mandy Zhao
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | | | - Vera Banning
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | - Zac Zwirko
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Amy Donahue
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Himisha Beltran
- Department of Medicine, Division of Hematology and Medical Oncology,
Weill Medical College of Cornell University, New York, New York, USA
- Institute for Precision Medicine, Weill Cornell Medical College and
New York-Presbyterian Hospital
| | - Juan Miguel Mosquera
- Institute for Precision Medicine, Weill Cornell Medical College and
New York-Presbyterian Hospital
- Department of Pathology and Laboratory Medicine, Weill Medical
College of Cornell University, New York, New York, USA
| | - Mark A Rubin
- Institute for Precision Medicine, Weill Cornell Medical College and
New York-Presbyterian Hospital
- Department of Pathology and Laboratory Medicine, Weill Medical
College of Cornell University, New York, New York, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New
York, New York, USA
| | - Cyrus V Hedvat
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New
York, New York, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New
York, New York, USA
| | - Lajos Pusztai
- Yale Cancer Center Genetics and Genomics Program, Yale School of
Medicine, New Haven, Connecticut, USA
| | | | - Chris Boshoff
- UCL Cancer Institute, University College London, London, UK
| | - Mirna Jarosz
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Alex Parker
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Jeffrey S Ross
- Foundation Medicine, Cambridge, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Albany Medical
College, Albany, New York, USA
| | - John Curran
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | - Doron Lipson
- Foundation Medicine, Cambridge, Massachusetts, USA
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148
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Latham GJ. Next-generation sequencing of formalin-fixed, paraffin-embedded tumor biopsies: navigating the perils of old and new technology to advance cancer diagnosis. Expert Rev Mol Diagn 2013; 13:769-72. [PMID: 24117229 DOI: 10.1586/14737159.2013.845090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gary J Latham
- Research & Technology Development, Asuragen, Inc., Austin, TX 78744, USA +1 512 681 5272 +1 512 681 5201
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149
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Malapelle U, Carlomagno C, de Luca C, Bellevicine C, Troncone G. KRAS testing in metastatic colorectal carcinoma: challenges, controversies, breakthroughs and beyond. J Clin Pathol 2013; 67:1-9. [DOI: 10.1136/jclinpath-2013-201835] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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150
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Sah S, Chen L, Houghton J, Kemppainen J, Marko AC, Zeigler R, Latham GJ. Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies. Genome Med 2013; 5:77. [PMID: 24001039 PMCID: PMC3978876 DOI: 10.1186/gm481] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/23/2013] [Indexed: 11/25/2022] Open
Abstract
The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing.
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