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Massaad E, Tabbarah A, Barmada M, Rbeiz J, Nasser S, Farra C. FISH analyses for 1p and 19q status on gliomas: Reporting an 8 years' experience from a tertiary care center in the Middle East. Ann Diagn Pathol 2022; 57:151899. [DOI: 10.1016/j.anndiagpath.2022.151899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/25/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022]
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Review of the genomic landscape of common pediatric CNS tumors and how data sharing will continue to shape this landscape in the future. Mol Biol Rep 2021; 48:7537-7544. [PMID: 34643931 DOI: 10.1007/s11033-021-06811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Over the past decade we have witnessed a rapid increase in our understanding of the molecular characteristics of pediatric central nervous system (CNS) tumors. Studies that utilize genomic sequencing have revealed a heterogeneous group of genetic drivers in pediatric CNS tumors including point mutations, gene fusions, and copy number alterations. This manuscript provides an overview of somatic genomic alterations in the most common pediatric CNS tumors including low grade gliomas, high grade gliomas, medulloblastomas, and ependymomas. Additionally, we will discuss the need and opportunity for genomic and clinical data sharing through the children's brain tumor network and other international initiatives.
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Williams EA, Sharaf R, Decker B, Werth AJ, Toma H, Montesion M, Sokol ES, Pavlick DC, Shah N, Williams KJ, Venstrom JM, Alexander BM, Ross JS, Albacker LA, Lin DI, Ramkissoon SH, Elvin JA. CDKN2C-Null Leiomyosarcoma: A Novel, Genomically Distinct Class of TP53/ RB1-Wild-Type Tumor With Frequent CIC Genomic Alterations and 1p/19q-Codeletion. JCO Precis Oncol 2020; 4:PO.20.00040. [PMID: 33015533 PMCID: PMC7529542 DOI: 10.1200/po.20.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Leiomyosarcoma (LMS) harbors frequent mutations in TP53 and RB1 but few actionable genomic alterations. Here, we searched for recurrent actionable genomic alterations in LMS that occur in the absence of common untreatable oncogenic drivers. METHODS Tissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS, were sequenced by hybrid-capture-based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant patient cases. RESULTS Overall, 77 LMS exhibited homozygous copy loss of CDKN2C at chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) in TP53, RB1, and ATRX were rare compared with the remainder of the LMS cohort (11.7% v 73.4%, 0% v 54.5%, 2.6% v 24.5%, respectively; all P < .0001). CDKN2C-null LMS patient cases were significantly enriched for GAs in CIC (40.3% v 1.4%) at 19q13.2, CDKN2A (46.8% v 7.0%), and RAD51B (16.9% v 1.7%; all P < .0001). Chromosome arm-level aneuploidy analysis of available LMS patient cases (n = 1,284) found that 81% (58 of 72) of CDKN2C-null LMS exhibited 1p/19q-codeletion, a significant enrichment compared with 5.1% in the remainder of the LMS cohort (P < .0001). In total, 99% of CDKN2C-null LMS were in women; the median age was 61 years at surgery (range, 36-81 years). Fifty-five patient cases were uterine primary, four were nonuterine, and the remaining 18 were of uncertain primary site. Sixty percent of cases showed at least focal epithelioid variant histology. Most patients had advanced-stage disease, with 62% of confirmed uterine primary LMS at International Federation of Gynecology and Obstetrics stage IVB. We further validated our findings in two publicly available datasets: The Cancer Genome Atlas and the Project GENIE initiative. CONCLUSION CDKN2C-null LMS defines a genomically distinct tumor that may have prognostic and/or therapeutic clinical implications, including possible use of specific cyclin-dependent kinase inhibitors.
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Affiliation(s)
| | | | - Brennan Decker
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Adrienne J. Werth
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | - Helen Toma
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | | | | | | | | | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | | | - Jeffrey S. Ross
- Foundation Medicine, Cambridge, MA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | | | | | - Shakti H. Ramkissoon
- Foundation Medicine, Cambridge, MA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
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Neill SG, Hauenstein J, Li MM, Liu YJ, Luo M, Saxe DF, Ligon AH. Copy number assessment in the genomic analysis of CNS neoplasia: An evidence-based review from the cancer genomics consortium (CGC) working group on primary CNS tumors. Cancer Genet 2020; 243:19-47. [PMID: 32203924 DOI: 10.1016/j.cancergen.2020.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
The period from the 1990s to the 2010s has witnessed a burgeoning sea change in the practice of surgical neuropathology due to the incorporation of genomic data into the assessment of a range of central nervous system (CNS) neoplasms. This change has since matured into the adoption of genomic information into the definition of several World Health Organization (WHO)-established diagnostic entities. The data needed to accomplish the modern diagnosis of CNS neoplasia includes DNA copy number aberrations that may be assessed through a variety of mechanisms. Through a review of the relevant literature and professional practice guidelines, here we provide a condensed and scored overview of the most critical DNA copy number aberrations to assess for a selection of primary CNS neoplasms.
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Affiliation(s)
- Stewart G Neill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer Hauenstein
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Marilyn M Li
- Department of Pathology, Division of Genomic Diagnostics, Children's Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA, United States
| | - Yajuan J Liu
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Minjie Luo
- Department of Pathology, Division of Genomic Diagnostics, Children's Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA, United States
| | - Debra F Saxe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Azra H Ligon
- Department of Pathology, Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, United States
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Pinkham M, Telford N, Whitfield G, Colaco R, O'Neill F, McBain C. FISHing Tips: What Every Clinician Should Know About 1p19q Analysis in Gliomas Using Fluorescence in situ Hybridisation. Clin Oncol (R Coll Radiol) 2015; 27:445-53. [DOI: 10.1016/j.clon.2015.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022]
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Parkinson DR, McCormack RT, Keating SM, Gutman SI, Hamilton SR, Mansfield EA, Piper MA, Deverka P, Frueh FW, Jessup JM, McShane LM, Tunis SR, Sigman CC, Kelloff GJ. Evidence of clinical utility: an unmet need in molecular diagnostics for patients with cancer. Clin Cancer Res 2014; 20:1428-44. [PMID: 24634466 DOI: 10.1158/1078-0432.ccr-13-2961] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article defines and describes best practices for the academic and business community to generate evidence of clinical utility for cancer molecular diagnostic assays. Beyond analytical and clinical validation, successful demonstration of clinical utility involves developing sufficient evidence to demonstrate that a diagnostic test results in an improvement in patient outcomes. This discussion is complementary to theoretical frameworks described in previously published guidance and literature reports by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, Institute of Medicine, and Center for Medical Technology Policy, among others. These reports are comprehensive and specifically clarify appropriate clinical use, adoption, and payer reimbursement for assay manufacturers, as well as Clinical Laboratory Improvement Amendments-certified laboratories, including those that develop assays (laboratory developed tests). Practical criteria and steps for establishing clinical utility are crucial to subsequent decisions for reimbursement without which high-performing molecular diagnostics will have limited availability to patients with cancer and fail to translate scientific advances into high-quality and cost-effective cancer care. See all articles in this CCR Focus section, "The Precision Medicine Conundrum: Approaches to Companion Diagnostic Co-development."
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Affiliation(s)
- David R Parkinson
- Authors' Affiliations: New Enterprise Associates, Inc., Menlo Park; CCS Associates, Mountain View; Myraqa, Redwood Shores, California; Johnson & Johnson/Veridex, LLC, Raritan, New Jersey; University of Texas, MD Anderson Cancer Center, Houston, Texas; Center for Diagnostics and Radiologic Health, Office of In Vitro Diagnostics, Personalized Medicine Program, Silver Spring; Center for Medical Technology Policy, Baltimore; Opus Three LLC; National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, Maryland; and Kaiser Permanente Research Affiliates Evidence-Based Practice Center, Kaiser Permanente Center for Health Research, Portland, Oregon
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Horbinski C. What do we know about IDH1/2 mutations so far, and how do we use it? Acta Neuropathol 2013; 125:621-36. [PMID: 23512379 DOI: 10.1007/s00401-013-1106-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/09/2013] [Indexed: 12/16/2022]
Abstract
Whole genome analyses have facilitated the discovery of clinically relevant genetic alterations in a variety of diseases, most notably cancer. A prominent example of this was the discovery of mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) in a sizeable proportion of gliomas and some other neoplasms. Herein the normal functions of these enzymes, how the mutations alter their catalytic properties, the effects of their D-2-hydroxyglutarate metabolite, technical considerations in diagnostic neuropathology, implications about prognosis and therapeutic considerations, and practical applications and controversies regarding IDH1/2 mutation testing are discussed.
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Affiliation(s)
- Craig Horbinski
- Department of Pathology, University of Kentucky, 307 Combs Cancer Research Facility, 800 Rose Street, Lexington, KY 40536, USA.
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