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BRCA1/2 Mutation Detection in the Tumor Tissue from Selected Polish Patients with Breast Cancer Using Next Generation Sequencing. Genes (Basel) 2021; 12:genes12040519. [PMID: 33918338 PMCID: PMC8065856 DOI: 10.3390/genes12040519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although, in the mutated BRCA detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare BRCA1/2 variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the BRCA1/2 genes. (3) Results: We detected nine pathogenic variants in 8 out of 75 selected patients (10.7%). We identified one somatic and eight germline variants. We also used different bioinformatic NGS software programs to analyze NGS FASTQ files and established that tertiary analysis performed with different tools was more likely to give the same outcome if we analyzed files received from secondary analysis using the same method. (4) Conclusions: Our study emphasizes (i) the importance of an NGS validation process with a bioinformatic procedure included; (ii) the importance of screening both somatic and germline pathogenic variants; (iii) the urgent need to identify additional susceptible genes in order to explain the high percentage of non-BRCA-related hereditary cases of breast cancer.
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2
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Christensen PA, Subedi S, Pepper K, Hendrickson HL, Li Z, Thomas JS, Long SW, Olsen RJ. Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data. JAMIA Open 2020; 3:299-305. [PMID: 32734171 PMCID: PMC7382636 DOI: 10.1093/jamiaopen/ooaa004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
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Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
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3
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Kang W, Kadri S, Puranik R, Wurst MN, Patil SA, Mujacic I, Benhamed S, Niu N, Zhen CJ, Ameti B, Long BC, Galbo F, Montes D, Iracheta C, Gamboa VL, Lopez D, Yourshaw M, Lawrence CA, Aisner DL, Fitzpatrick C, McNerney ME, Wang YL, Andrade J, Volchenboum SL, Furtado LV, Ritterhouse LL, Segal JP. System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management. J Mol Diagn 2018; 20:522-532. [PMID: 29698836 PMCID: PMC6039793 DOI: 10.1016/j.jmoldx.2018.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/01/2018] [Accepted: 03/29/2018] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory (SIMPL), a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. SIMPL was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of SIMPL, its clinical validation at University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing.
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Affiliation(s)
- Wenjun Kang
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Sabah Kadri
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Rutika Puranik
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Michelle N Wurst
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Sushant A Patil
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Ibro Mujacic
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Sonia Benhamed
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Nifang Niu
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Chao Jie Zhen
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Bekim Ameti
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Bradley C Long
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Filipo Galbo
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - David Montes
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Crystal Iracheta
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Venessa L Gamboa
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Daisy Lopez
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Michael Yourshaw
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Carolyn A Lawrence
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Dara L Aisner
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Carrie Fitzpatrick
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Megan E McNerney
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois; Comprehensive Cancer Center, The University of Chicago Medicine, Chicago, Illinois
| | - Y Lynn Wang
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Samuel L Volchenboum
- Center for Research Informatics, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Larissa V Furtado
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Lauren L Ritterhouse
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois; Informatics Subdivision Leadership, Association for Molecular Pathology, Bethesda, Maryland.
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4
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Epithelial-Myoepithelial Carcinoma: Frequent Morphologic and Molecular Evidence of Preexisting Pleomorphic Adenoma, Common HRAS Mutations in PLAG1-intact and HMGA2-intact Cases, and Occasional TP53, FBXW7, and SMARCB1 Alterations in High-grade Cases. Am J Surg Pathol 2017; 42:18-27. [PMID: 29135520 DOI: 10.1097/pas.0000000000000933] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We hypothesized that there is a relationship between the preexisting pleomorphic adenoma [PA]), histologic grade of epithelial-myoepithelial carcinomas (EMCAs), and genetic alterations. EMCAs (n=39) were analyzed for morphologic and molecular evidence of preexisting PA (PLAG1, HMGA2 status by fluorescence in situ hybridization, FISH, and FGFR1-PLAG1 fusion by next-generation sequencing, NGS). Twenty-three EMCAs were further analyzed by NGS for mutations and copy number variation in 50 cancer-related genes. On the basis of combined morphologic and molecular evidence of PA, the following subsets of EMCA emerged: (a) EMCAs with morphologic evidence of preexisting PA, but intact PLAG1 and HMGA2 (12/39, 31%), (b) Carcinomas with PLAG1 alterations (9/39, 23%), or (c) HMGA2 alterations (10/39, 26%), and (d) de novo carcinomas, without morphologic or molecular evidence of PA (8/39, 21%). Twelve high-grade EMCAs (12/39, 31%) occurred across all subsets. The median disease-free survival was 80 months (95% confidence interval, 77-84 mo). Disease-free survival and other clinicopathologic parameters did not differ by the above defined subsets. HRAS mutations were more common in EMCAs with intact PLAG1 and HMGA2 (7/9 vs. 1/14, P<0.001). Other genetic abnormalities (TP53 [n=2], FBXW7 [n=1], SMARCB1 deletion [n=1]) were seen only in high-grade EMCAs with intact PLAG1 and HMGA2. We conclude that most EMCAs arose ex PA (31/39, 80%) and the genetic profile of EMCA varies with the absence or presence of preexisting PA and its cytogenetic signature. Progression to higher grade EMCA with intact PLAG1 and HMGA2 correlates with the presence of TP53, FBXW7 mutations, or SMARCB1 deletion.
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5
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Mehrad M, Roy S, Bittar HT, Dacic S. Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations. Arch Pathol Lab Med 2017; 142:353-357. [DOI: 10.5858/arpa.2017-0046-oa] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance.
Objective.—
To determine the best testing algorithm for patients with lung cancer in our clinical practice.
Design.—
Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel.
Results.—
Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations.
Conclusions.—
The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.
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Affiliation(s)
| | | | | | - Sanja Dacic
- From the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee (Dr Mehrad); and the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Drs Roy, Trejo Bittar, and Dacic)
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6
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Roy S, Pradhan D, Ernst WL, Mercurio S, Najjar Y, Parikh R, Parwani AV, Pai RK, Dhir R, Nikiforova MN. Next-generation sequencing-based molecular characterization of primary urinary bladder adenocarcinoma. Mod Pathol 2017; 30:1133-1143. [PMID: 28548125 DOI: 10.1038/modpathol.2017.33] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/24/2022]
Abstract
Primary bladder adenocarcinoma is a rare and aggressive tumor with poor clinical outcomes and no standard of care therapy. Molecular biology of this tumor is unknown due to the lack of comprehensive molecular profiling studies. The study aimed to identify genomic alterations of clinical and therapeutic significance using next-generation sequencing and compare genomic profile of primary bladder adenocarcinoma with that of high-grade urothelial carcinoma and colorectal adenocarcinoma. A cohort of 15 well-characterized primary bladder adenocarcinoma was subjected to targeted next-generation sequencing for the identification of mutations and copy-number changes in 51 cancer-related genes. Genomic profiles of 25 HGUCs and 25 colorectal adenocarcinomas using next-generation sequencing of 50 genes were compared with primary bladder adenocarcinoma. Genomic profiles were visualized using JavaScript library D3.js. A striking finding was the distinct lack of genomic alterations across the 51 genes assessed in mucinous subtype of primary bladder adenocarcinoma. Eleven of 15 primary bladder adenocarcinoma harbored at least one genomic alteration in TP53, KRAS, PIK3CA, CTNNB1, APC, TERT, FBXW7, IDH2 and RB1, many of which are novel findings and of potential therapeutic significance. CTNNB1 and APC mutations were restricted to enteric subtype only. While genomic alterations of primary bladder adenocarcinoma showed substantial overlap with colorectal adenocarcinoma, FGFR3 and HRAS mutations and APC, CTNNB1 and IDH2 alterations were mutually exclusive between primary bladder adenocarcinoma and high-grade urothelial carcinoma. These alterations affecting the MAP kinase, PI3K/Akt, Wnt, IDH (metabolic) and Tp53/Rb1 signaling pathways may provide the opportunity for defining targeted therapeutic approaches.
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Affiliation(s)
- Somak Roy
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Dinesh Pradhan
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wayne L Ernst
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stephanie Mercurio
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yana Najjar
- Department of Medical Oncology and Hematology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rahul Parikh
- Department of Medical Oncology and Hematology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Pathology, Ohio State University, Columbus, OH, USA
| | - Reetesh K Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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7
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Doig KD, Fellowes A, Bell AH, Seleznev A, Ma D, Ellul J, Li J, Doyle MA, Thompson ER, Kumar A, Lara L, Vedururu R, Reid G, Conway T, Papenfuss AT, Fox SB. PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. Genome Med 2017; 9:38. [PMID: 28438193 PMCID: PMC5404673 DOI: 10.1186/s13073-017-0427-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout. These capabilities must be packaged in software that integrates the disparate components into a useable system. Results To meet these needs, we developed a web-based application, PathOS, which takes variant data from a patient sample through to a clinical report. PathOS has been used operationally in the Peter MacCallum Cancer Centre for two years for the analysis, curation and reporting of genetic tests for cancer patients, as well as the curation of large-scale research studies. PathOS has also been deployed in cloud environments allowing multiple institutions to use separate, secure and customisable instances of the system. Increasingly, the bottleneck of variant curation is limiting the adoption of clinical sequencing for molecular diagnostics. PathOS is focused on providing clinical variant curators and pathology laboratories with a decision support system needed for personalised medicine. While the genesis of PathOS has been within cancer molecular diagnostics, the system is applicable to NGS clinical reporting generally. Conclusions The widespread availability of genomic sequencers has highlighted the limited availability of software to support clinical decision-making in molecular pathology. PathOS is a system that has been developed and refined in a hospital laboratory context to meet the needs of clinical diagnostics. The software is available as a set of Docker images and source code at https://github.com/PapenfussLab/PathOS. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0427-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenneth D Doig
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. .,Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia.
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Anthony H Bell
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Andrei Seleznev
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - David Ma
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Jason Ellul
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Jason Li
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Maria A Doyle
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Ella R Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amit Kumar
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia
| | - Luis Lara
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Ravikiran Vedururu
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Gareth Reid
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Thomas Conway
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
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8
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Cantara S, Marzocchi C, Pilli T, Cardinale S, Forleo R, Castagna MG, Pacini F. Molecular Signature of Indeterminate Thyroid Lesions: Current Methods to Improve Fine Needle Aspiration Cytology (FNAC) Diagnosis. Int J Mol Sci 2017; 18:ijms18040775. [PMID: 28383480 PMCID: PMC5412359 DOI: 10.3390/ijms18040775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023] Open
Abstract
Fine needle aspiration cytology (FNAC) represents the gold standard for determining the nature of thyroid nodules. It is a reliable method with good sensitivity and specificity. However, indeterminate lesions remain a diagnostic challenge and researchers have contributed molecular markers to search for in cytological material to refine FNAC diagnosis and avoid unnecessary surgeries. Nowadays, several "home-made" methods as well as commercial tests are available to investigate the molecular signature of an aspirate. Moreover, other markers (i.e., microRNA, and circulating tumor cells) have been proposed to discriminate benign from malignant thyroid lesions. Here, we review the literature and provide data from our laboratory on mutational analysis of FNAC material and circulating microRNA expression obtained in the last 6 years.
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Affiliation(s)
- Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Carlotta Marzocchi
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Tania Pilli
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Sandro Cardinale
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Raffaella Forleo
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Maria Grazia Castagna
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Furio Pacini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
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9
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Bhargava R, Florea AV, Pelmus M, Jones MW, Bonaventura M, Wald A, Nikiforova M. Breast Tumor Resembling Tall Cell Variant of Papillary Thyroid Carcinoma: A Solid Papillary Neoplasm With Characteristic Immunohistochemical Profile and Few Recurrent Mutations. Am J Clin Pathol 2017; 147:399-410. [PMID: 28375433 DOI: 10.1093/ajcp/aqx016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Breast tumor resembling tall cell variant of papillary thyroid carcinoma (BTRPTC) is a rare breast lesion that is unrelated to thyroid carcinoma. Morphologically, it shows a solid papillary lesion with bland cytology, eosinophilic/amphophilic secretions, nuclear grooves, reversal of nuclear polarity (recently described), and nuclear inclusions. Clinical course is often uneventful with few exceptions reported in the literature. Herein, we report three additional cases. METHODS Immunohistochemical staining and next-generation sequencing was performed on all three cases. RESULTS The lesional cells on all cases were positive for cytokeratin 5 and S100, with weak expression/lack of estrogen receptor. No staining was observed for myoepithelial markers (p63 and myosin heavy chain) around the lesion. IDH2 mutations were identified in two cases at nucleotide 172 (cases 1 and 3). ATM gene mutation was identified in cases 2 and 3 and PIK3CA mutation in case 3. All patients are currently without disease. CONCLUSIONS BTRPTC is a slow-growing neoplastic lesion that needs to be distinguished from other papillary lesions for optimizing therapy.
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Affiliation(s)
- Rohit Bhargava
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | | | - Miroslawa W Jones
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Marguerite Bonaventura
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Abigail Wald
- University of Pittsburgh Medical Center-Presbyterian, Pittsburgh, PA
| | - Marina Nikiforova
- University of Pittsburgh Medical Center-Presbyterian, Pittsburgh, PA
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10
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Roy-Chowdhuri S, Roy S, Monaco SE, Routbort MJ, Pantanowitz L. Big data from small samples: Informatics of next-generation sequencing in cytopathology. Cancer Cytopathol 2016; 125:236-244. [PMID: 27918649 DOI: 10.1002/cncy.21805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 12/12/2022]
Abstract
The rapid adoption of next-generation sequencing (NGS) in clinical molecular laboratories has redefined the practice of cytopathology. Instead of simply being used as a diagnostic tool, cytopathology has evolved into a practice providing important genomic information that guides clinical management. The recent emphasis on maximizing limited-volume cytology samples for ancillary molecular studies, including NGS, requires cytopathologists not only to be more involved in specimen collection and processing techniques but also to be aware of downstream testing and informatics issues. For the integration of molecular informatics into the clinical workflow, it is important to understand the computational components of the NGS workflow by which raw sequence data are transformed into clinically actionable genomic information and to address the challenges of having a robust and sustainable informatics infrastructure for NGS-based testing in a clinical environment. Adapting to needs ranging from specimen procurement to report delivery is crucial for the optimal utilization of cytology specimens to accommodate requests from clinicians to improve patient care. This review presents a broad overview of the various aspects of informatics in the context of NGS-based testing of cytology specimens. Cancer Cytopathol 2017;125:236-244. © 2016 American Cancer Society.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Somak Roy
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sara E Monaco
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mark J Routbort
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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Roy S, Pfeifer JD, LaFramboise WA, Pantanowitz L. Molecular digital pathology: progress and potential of exchanging molecular data. Expert Rev Mol Diagn 2016; 16:941-7. [PMID: 27471996 DOI: 10.1080/14737159.2016.1206472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many of the demands to perform next generation sequencing (NGS) in the clinical laboratory can be resolved using the principles of telepathology. Molecular telepathology can allow facilities to outsource all or a portion of their NGS operation such as cloud computing, bioinformatics pipelines, variant data management, and knowledge curation. Clinical pathology laboratories can electronically share diverse types of molecular data with reference laboratories, technology service providers, and/or regulatory agencies. Exchange of electronic molecular data allows laboratories to perform validation of rare diseases using foreign data, check the accuracy of their test results against benchmarks, and leverage in silico proficiency testing. This review covers the emerging subject of molecular telepathology, describes clinical use cases for the appropriate exchange of molecular data, and highlights key issues such as data integrity, interoperable formats for massive genomic datasets, security, malpractice and emerging regulations involved with this novel practice.
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Affiliation(s)
- Somak Roy
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| | - John D Pfeifer
- b Department of Pathology , Washington University , St Louis , MO , USA
| | - William A LaFramboise
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| | - Liron Pantanowitz
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
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12
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Palmisano A, Zhao Y, Li MC, Polley EC, Simon RM. OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials. Brief Bioinform 2016; 18:723-734. [DOI: 10.1093/bib/bbw059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 12/16/2022] Open
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13
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Cutting E, Banchero M, Beitelshees AL, Cimino JJ, Fiol GD, Gurses AP, Hoffman MA, Jeng LJB, Kawamoto K, Kelemen M, Pincus HA, Shuldiner AR, Williams MS, Pollin TI, Overby CL. User-centered design of multi-gene sequencing panel reports for clinicians. J Biomed Inform 2016; 63:1-10. [PMID: 27423699 DOI: 10.1016/j.jbi.2016.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 11/15/2022]
Abstract
The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects.
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Affiliation(s)
- Elizabeth Cutting
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Meghan Banchero
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Amber L Beitelshees
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - James J Cimino
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States
| | - Ayse P Gurses
- Division of Health Sciences Informatics, Johns Hopkins University School of Medicine, United States; Armstrong Institute for Patient Safety and Quality, Johns Hopkins University School of Medicine, United States; Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, United States
| | - Mark A Hoffman
- University of Missouri - Kansas City, Kansas City, MO, United States; Children's Mercy Hospital, Kansas City, MO, United States
| | - Linda Jo Bone Jeng
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States; Departments of Medicine, Pathology and Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States
| | - Mark Kelemen
- University of Maryland Medical Center, Baltimore, MD, United States
| | - Harold Alan Pincus
- Columbia University and New York-Presbyterian Hospital, New York, NY, United States
| | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, United States
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Casey Lynnette Overby
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States; Division of Health Sciences Informatics, Johns Hopkins University School of Medicine, United States; Division of General Internal Medicine, Johns Hopkins University School of Medicine, United States.
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14
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Chiosea SI, Thompson LDR, Weinreb I, Bauman JE, Mahaffey AM, Miller C, Ferris RL, Gooding WE. Subsets of salivary duct carcinoma defined by morphologic evidence of pleomorphic adenoma, PLAG1 or HMGA2 rearrangements, and common genetic alterations. Cancer 2016; 122:3136-3144. [PMID: 27379604 DOI: 10.1002/cncr.30179] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/28/2016] [Accepted: 06/01/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND The authors hypothesized that histogenetic classification of salivary duct carcinoma (SDC) could account for de novo tumors and those with morphologic or molecular evidence (pleomorphic adenoma gene 1 [PLAG1], high-mobility group AT hook 2 [HMGA2] rearrangement, amplification) of pleomorphic adenoma (PA). METHODS SDCs (n = 66) were reviewed for morphologic evidence of PA. PLAG1 and HMGA2 alterations were detected by fluorescence in situ hybridization (FISH). PLAG1-positive tumors were tested by FISH for fibroblast growth factor receptor 1 (FGFR1) rearrangement. Thirty-nine tumors were analyzed using a commercial panel for mutations and copy number variations in 50 cancer-related genes. RESULTS On the basis of combined morphologic and molecular evidence of PA, 4 subsets of SDC emerged: 1) carcinomas with morphologic evidence of PA but intact PLAG1 and HMGA2 (n = 22); 2) carcinomas with PLAG1 alteration (n = 18) or 3) HMGA2 alteration (n = 12); and 4) de novo carcinomas, without morphologic or molecular evidence of PA (n = 14). The median disease-free survival was 37 months (95% confidence interval, 28.4-45.6 months). Disease-free survival and other clinicopathologic parameters did not differ for the subsets defined above. Combined Harvey rat sarcoma viral oncogene homolog/phosphatidylinositol-4,5-biphosphate 3-kinase, catalytic subunit α (HRAS/PIK3CA) mutations were observed predominantly in de novo carcinomas (5 of 8 vs 2 of 31 tumors; P = .035). Erb-B2 receptor tyrosine kinase 2 (ERBB2) copy number gain was not observed in de novo carcinomas (0 of 8 vs 12 of 31 tumors; P = .08). Tumor protein 53 (TP53) mutations were more common in SDC ex pleomorphic adenomas than in de novo carcinomas (17 of 31 vs 1 of 8 tumors; P = .033). CONCLUSIONS The genetic profile of SDC varies with the absence or presence of pre-existing PA and its cytogenetic signature. Most de novo SDCs harbor combined HRAS/PIK3CA mutations and no ERBB2 amplification. Cancer 2016;122:3136-44. © 2016 American Cancer Society.
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Affiliation(s)
- Simion I Chiosea
- Depatment of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
| | - Lester D R Thompson
- Department of Pathology, Southern California Permanente Medical Group, Woodland Hills, California
| | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Julie E Bauman
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Alyssa M Mahaffey
- Depatment of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Caitlyn Miller
- Depatment of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Robert L Ferris
- Division of Head and Neck Surgery, Department of Otolaryngology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - William E Gooding
- Biostatistics Facility, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
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Zhang X. Value of Molecular Tests in Cytologically Indeterminate Lesions of Thyroid. Arch Pathol Lab Med 2016; 139:1484-90. [PMID: 26619020 DOI: 10.5858/arpa.2014-0245-ra] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Fine-needle aspiration has been the initial step in the workup of thyroid nodular lesions and has successfully reduced the number of unnecessary surgeries and improved preoperative malignancy detection. However, up to one-third of cases fall in the diagnostically "indeterminate group," which poses a patient-management challenge. objective: To review the characteristics of molecular tests useful for stratifying the malignancy risk of indeterminate thyroid lesions, including their advantages and limitations. DATA SOURCES PubMed. CONCLUSIONS Molecular tests are useful for triage of indeterminate thyroid nodules initially diagnosed by using fine-needle aspiration. Immunocytochemistry is readily available with the shortest turnaround time among the molecular tests but suffers from poor reproducibility and low interpretation concordance. Gene mutation analysis is superior in detecting malignancies as a rule-in test, despite low specificity. Next-generation sequencing seems promising but needs more validations before widespread use. Gene expression profiling is more suitable for detecting benign lesions as a rule-out test to avoid unnecessary surgeries but is not reliable in excluding malignancies. MicroRNA profiling has great potential for both risk stratification and predicting prognosis but is limited by significant variations in sensitivity and specificity. Although many questions still need to be answered, taken together, molecular tests are a promising option for classifying cytologically indeterminate thyroid nodular lesions.
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Affiliation(s)
- Xinmin Zhang
- From the Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania
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Roy S, LaFramboise WA, Nikiforov YE, Nikiforova MN, Routbort MJ, Pfeifer J, Nagarajan R, Carter AB, Pantanowitz L. Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment. Arch Pathol Lab Med 2016; 140:958-75. [PMID: 26901284 DOI: 10.5858/arpa.2015-0507-ra] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT -Next-generation sequencing (NGS) is revolutionizing the discipline of laboratory medicine, with a deep and direct impact on patient care. Although it empowers clinical laboratories with unprecedented genomic sequencing capability, NGS has brought along obvious and obtrusive informatics challenges. Bioinformatics and clinical informatics are separate disciplines with typically a small degree of overlap, but they have been brought together by the enthusiastic adoption of NGS in clinical laboratories. The result has been a collaborative environment for the development of novel informatics solutions. Sustaining NGS-based testing in a regulated clinical environment requires institutional support to build and maintain a practical, robust, scalable, secure, and cost-effective informatics infrastructure. OBJECTIVE -To discuss the novel NGS informatics challenges facing pathology laboratories today and offer solutions and future developments to address these obstacles. DATA SOURCES -The published literature pertaining to NGS informatics was reviewed. The coauthors, experts in the fields of molecular pathology, precision medicine, and pathology informatics, also contributed their experiences. CONCLUSIONS -The boundary between bioinformatics and clinical informatics has significantly blurred with the introduction of NGS into clinical molecular laboratories. Next-generation sequencing technology and the data derived from these tests, if managed well in the clinical laboratory, will redefine the practice of medicine. In order to sustain this progress, adoption of smart computing technology will be essential. Computational pathologists will be expected to play a major role in rendering diagnostic and theranostic services by leveraging "Big Data" and modern computing tools.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Liron Pantanowitz
- From the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Drs Roy, LaFramboise, Nikiforov, Nikiforova, and Pantanowitz); the Department of Pathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); the Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri (Drs Pfeifer and Nagarajan); PierianDx, St Louis, Missouri (Dr Nagarajan); and the Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (Dr Carter)
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17
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Abstract
Contemporary classification and treatment of salivary duct carcinoma (SDC) require its thorough molecular characterization. Thirty apocrine SDCs were analyzed by the Ion Ampliseq Cancer HotSpot panel v2 for mutations in 50 cancer-related genes. Mutational findings were corroborated by immunohistochemistry (eg, TP53, BRAF, β-catenin, estrogen, and androgen receptors) or Sanger sequencing/SNaPshot polymerase chain reaction. ERBB2 (HER2), PTEN, FGFR1, CDKN2A/P16, CMET, EGFR, MDM2, and PIK3CA copy number changes were studied by fluorescence in situ hybridization. TP53 mutations (15/27, 56%), PTEN loss (11/29, 38%, including 2 cases with PTEN mutation), PIK3CA hotspot mutations (10/30, 33%), HRAS hotspot mutations (10/29; 34%), and ERBB2 amplification (9/29, 31%, including 1 case with mutation) represented the 5 most common abnormalities. There was no correlation between genetic changes and clinicopathologic parameters. There was substantial overlap between genetic changes: 8 of 9 cases with ERBB2 amplification also harbored a PIK3CA, HRAS, and TP53 mutation and/or PTEN loss. Six of 10 cases with PIK3CA mutation also had an HRAS mutation. These findings provide a molecular rationale for dual targeting of mitogen-activated protein kinase and phosphoinositide 3-kinase pathways in SDC. FGFR1 amplification (3/29, 10%) represents a new potential target. On the basis of studies of breast carcinomas, the efficacy of anti-ERBB2 therapy will likely be decreased in SDC with ERBB2 amplification co-occurring with PIK3CA mutation or PTEN loss. Therefore, isolated ERBB2 testing is insufficient for theranostic stratification of apocrine SDC. On the basis of the prevalence and type of genetic changes, apocrine SDC appears to resemble one subtype of breast carcinoma-"luminal androgen receptor positive/molecular apocrine."
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18
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Ji JH, Oh YL, Hong M, Yun JW, Lee HW, Kim D, Ji Y, Kim DH, Park WY, Shin HT, Kim KM, Ahn MJ, Park K, Sun JM. Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer. PLoS Genet 2015; 11:e1005467. [PMID: 26295973 PMCID: PMC4546689 DOI: 10.1371/journal.pgen.1005467] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/24/2015] [Indexed: 01/12/2023] Open
Abstract
The genetic landscape of medullary thyroid cancer (MTC) is not yet fully understood, although some oncogenic mutations have been identified. To explore genetic profiles of MTCs, formalin-fixed, paraffin-embedded tumor tissues from MTC patients were assayed on the Ion AmpliSeq Cancer Panel v2. Eighty-four sporadic MTC samples and 36 paired normal thyroid tissues were successfully sequenced. We discovered 101 hotspot mutations in 18 genes in the 84 MTC tissue samples. The most common mutation was in the ret proto-oncogene, which occurred in 47 cases followed by mutations in genes encoding Harvey rat sarcoma viral oncogene homolog (N = 14), serine/threonine kinase 11 (N = 11), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (N = 6), mutL homolog 1 (N = 4), Kiesten rat sarcoma viral oncogene homolog (N = 3) and MET proto-oncogene (N = 3). We also evaluated anaplastic lymphoma kinase (ALK) rearrangement by immunohistochemistry and break-apart fluorescence in situ hybridization (FISH). Two of 98 screened cases were positive for ALK FISH. To identify the genomic breakpoint and 5’ fusion partner of ALK, customized targeted cancer panel sequencing was performed using DNA from tumor samples of the two patients. Glutamine:fructose-6-phosphate transaminase 1 (GFPT1)-ALK and echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusions were identified. Additional PCR analysis, followed by Sanger sequencing, confirmed the GFPT1-ALK fusion, indicating that the fusion is a result of intra-chromosomal translocation or deletion. Notably, a metastatic MTC case harboring the EML4-ALK fusion showed a dramatic response to an ALK inhibitor, crizotinib. In conclusion, we found several genetic mutations in MTC and are the first to identify ALK fusions in MTC. Our results suggest that the EML4-ALK fusion in MTC may be a potential driver mutation and a valid target of ALK inhibitors. Furthermore, the GFPT1-ALK fusion may be a potential candidate for molecular target therapy. Little is known about the molecular biology of medullary thyroid cancer (MTC), which is a rare disease. Genomics are increasingly being used to improve our knowledge about disease biology and to identify therapeutic targets in many cancers. Here, we report the largest genomic results of MTC to date. MTC tissue frequently included several mutations. For the first time, anaplastic lymphoma kinase (ALK) rearrangements were detected in MTC: one case with a glutamine:fructose-6-phosphate transaminase 1 (GFPT1)-ALK fusion, and another case with an echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion. The fusion mechanism of the novel GFPT1-ALK fusion was successfully investigated using molecular biology techniques. In addition, an inhibitor of ALK (crizotinib) dramatically decreased the number of metastatic MTC lesions harboring the EML4-ALK fusion, thus verifying the fusion as a promising target in MTC. Our findings suggest that using rapidly improving sequencing techniques and accumulated genomic data to comprehensively perform genetic analyses on rare tumors, such as MTC, will help to improve the poor prognosis of orphan diseases.
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Affiliation(s)
- Jun Ho Ji
- Division of Hematology and Oncology, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Young Lyun Oh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mineui Hong
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Won Yun
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hyun-Woo Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - DeokGeun Kim
- Molecular Translational Research Center, Samsung Biomedical Research Institute, Seoul, Korea
| | - Yongick Ji
- Molecular Translational Research Center, Samsung Biomedical Research Institute, Seoul, Korea
| | - Duk-Hwan Kim
- Molecular Translational Research Center, Samsung Biomedical Research Institute, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Myung-Ju Ahn
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keunchil Park
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Mu Sun
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
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19
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Zhao Y, Polley EC, Li MC, Lih CJ, Palmisano A, Sims DJ, Rubinstein LV, Conley BA, Chen AP, Williams PM, Kummar S, Doroshow JH, Simon RM. GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials. Cancer Inform 2015; 14:45-55. [PMID: 25861217 PMCID: PMC4368061 DOI: 10.4137/cin.s17282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/21/2014] [Accepted: 12/25/2014] [Indexed: 12/22/2022] Open
Abstract
We have developed an informatics system, GeneMed, for the National Cancer Institute (NCI) molecular profiling-based assignment of cancer therapy (MPACT) clinical trial (NCT01827384) being conducted in the National Institutes of Health (NIH) Clinical Center. This trial is one of the first to use a randomized design to examine whether assigning treatment based on genomic tumor screening can improve the rate and duration of response in patients with advanced solid tumors. An analytically validated next-generation sequencing (NGS) assay is applied to DNA from patients’ tumors to identify mutations in a panel of genes that are thought likely to affect the utility of targeted therapies available for use in the clinical trial. The patients are randomized to a treatment selected to target a somatic mutation in the tumor or with a control treatment. The GeneMed system streamlines the workflow of the clinical trial and serves as a communications hub among the sequencing lab, the treatment selection team, and clinical personnel. It automates the annotation of the genomic variants identified by sequencing, predicts the functional impact of mutations, identifies the actionable mutations, and facilitates quality control by the molecular characterization lab in the review of variants. The GeneMed system collects baseline information about the patients from the clinic team to determine eligibility for the panel of drugs available. The system performs randomized treatment assignments under the oversight of a supervising treatment selection team and generates a patient report containing detected genomic alterations. NCI is planning to expand the MPACT trial to multiple cancer centers soon. In summary, the GeneMed system has been proven to be an efficient and successful informatics hub for coordinating the reliable application of NGS to precision medicine studies.
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Affiliation(s)
- Yingdong Zhao
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Eric C Polley
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Ming-Chung Li
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Chih-Jian Lih
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alida Palmisano
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - David J Sims
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence V Rubinstein
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Barbara A Conley
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - P Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Richard M Simon
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
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20
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Dumur CI, Kraft AO. Next-generation sequencing and the cytopathologist. Cancer Cytopathol 2014; 123:69-70. [PMID: 25557465 DOI: 10.1002/cncy.21515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 12/10/2014] [Indexed: 11/07/2022]
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Abstract
Thyroid nodules are common, and the accurate diagnosis of cancer or benign disease is important for the effective clinical management of patients. Molecular markers are a helpful diagnostic tool, particularly for cytologically indeterminate thyroid nodules. In the past few years, significant progress has been made in developing molecular markers for clinical use in fine-needle aspiration specimens, including gene mutation panels and gene expression classifiers. With the availability of next generation sequencing technology, gene mutation panels can be expanded to interrogate multiple genes simultaneously and to provide yet more accurate diagnostic information. In addition, recently several new molecular markers of thyroid cancer have been identified that offer diagnostic, prognostic, and therapeutic information that might be of value in guiding individualized management of patients with thyroid nodules.
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Affiliation(s)
- Susan J Hsiao
- Division of Molecular and Genomic PathologyDepartment of Pathology, University of Pittsburgh School of Medicine, 3477 Euler Way, Room 8031, Pittsburgh, Pennsylvania 15213, USA
| | - Yuri E Nikiforov
- Division of Molecular and Genomic PathologyDepartment of Pathology, University of Pittsburgh School of Medicine, 3477 Euler Way, Room 8031, Pittsburgh, Pennsylvania 15213, USA
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22
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Dumur CI. Available resources and challenges for the clinical annotation of somatic variations. Cancer Cytopathol 2014; 122:730-6. [PMID: 25111663 PMCID: PMC4231254 DOI: 10.1002/cncy.21471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a number of such resources that have been designed to catalog and mine a plethora of germline variants or mutations. However, when analyzing tumor specimens in clinical settings, one may need to use different or ancillary resources that are specific for somatic variants or actionable mutations that may have clinical or treatment implications. The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology. In addition, the current need for collating various annotation sources into one-stop solutions to facilitate faster query execution and better integration into existing laboratory information systems are discussed.
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Affiliation(s)
- Catherine I Dumur
- Department of Pathology, Virginia Commonwealth UniversityRichmond, Virginia
- Corresponding author: Catherine I. Dumur, PhD, Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA 23298; Fax: (804) 827-4738;
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