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Williams EA, Vegas I, El-Senduny FF, Zhang J, Mata DA, Hiemenz MC, Hughes SR, Sa BC, Kraft GP, Gorbatov N, Foley-Peres K, Sanchez EZ, Milikowski C, Williams KJ, Ross JS, Kurzrock R, Montgomery EA, Lombard DB, Kumar S. Pan-cancer Genomic Analysis of AXL Mutations Reveals a Novel, Recurrent, Functionally Activating AXL W451C Alteration Specific to Myxofibrosarcoma. Am J Surg Pathol 2024; 48:699-707. [PMID: 38369783 PMCID: PMC11093512 DOI: 10.1097/pas.0000000000002191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Myxofibrosarcoma (MFS) is a common soft tissue sarcoma of the elderly that typically shows low tumor mutational burden, with mutations in TP53 and in genes associated with cell cycle checkpoints ( RB1 , CDKN2A ). Unfortunately, no alterations or markers specific to MFS have been identified and, as a consequence, there are no effective targeted therapies. The receptor tyrosine kinase AXL, which drives cellular proliferation, is targetable by new antibody-based therapeutics. Expression of AXL messenger RNA is elevated in a variety of sarcoma types, with the highest levels reported in MFS, but the pathogenic significance of this finding remains unknown. To assess a role for AXL abnormalities in MFS, we undertook a search for AXL genomic alterations in a comprehensive genomic profiling database of 463,546 unique tumors (including 19,879 sarcomas, of which 315 were MFS) interrogated by targeted next-generation DNA and/or RNA sequencing. Notably, the only genomic alterations recurrent in a specific sarcoma subtype were AXL W451C (n = 8) and AXL W450C (n = 2) mutations. The tumors involved predominantly older adults (age: 44 to 81 [median: 72] y) and histologically showed epithelioid and spindle-shaped cells in a variably myxoid stroma, with 6 cases diagnosed as MFS, 3 as undifferentiated pleomorphic sarcoma (UPS), and 1 as low-grade sarcoma. The AXL W451C mutation was not identified in any non-sarcoma malignancy. A review of publicly available data sets revealed a single AXL W451C-mutant case of UPS that clustered with MFS/UPS by methylation profiling. Functional studies revealed a novel activation mechanism: the W451C mutation causes abnormal unregulated dimerization of the AXL receptor tyrosine kinase through disulfide bond formation between pairs of mutant proteins expressing ectopic cysteine residues. This dimerization triggers AXL autophosphorylation and activation of downstream ERK signaling. We further report sarcomas of diverse histologic subtypes with AXL gene amplifications, with the highest frequency of amplification identified in MFS cases without the W451C mutation. In summary, the activating AXL W451C mutation appears highly specific to MFS, with a novel mechanism to drive unregulated signaling. Moreover, AXL gene amplifications and messenger RNA overexpression are far more frequent in MFS than in other sarcoma subtypes. We conclude that these aberrations in AXL are distinct features of MFS and may aid diagnosis, as well as the selection of available targeted therapies.
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Affiliation(s)
- Erik A. Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
- Department of Pathology, Jackson Memorial Hospital, Miami, FL
| | - Isabella Vegas
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - Fardous F. El-Senduny
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - Jessica Zhang
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | | | | | | | - Brianna C. Sa
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - Garrett P. Kraft
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - Nicole Gorbatov
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | | | | | - Clara Milikowski
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Jeffrey S. Ross
- Department of Pathology, Jackson Memorial Hospital, Miami, FL
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | - Razelle Kurzrock
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Elizabeth A. Montgomery
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
| | - David B. Lombard
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
- Department of Pathology, Jackson Memorial Hospital, Miami, FL
- Department of Pathology, Miami VA Healthcare System, Miami, FL
| | - Surinder Kumar
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center
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Neal JW, Minichiello K, Brennick R, Huang RSP, Hiemenz MC, Amler C, Patel J, Herbst R, Reckamp KL, Borghaei H, Highleyman L, Redman MW, Pasquina LW, Kozono DE. A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol. Oncologist 2024:oyae062. [PMID: 38597608 DOI: 10.1093/oncolo/oyae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
For cancer clinical trials that require central confirmation of tumor genomic profiling, exhaustion of tissue from standard-of-care testing may prevent enrollment. For Lung-MAP, a master protocol that requires results from a defined centralized clinical trial assay to assign patients to a therapeutic substudy, we developed a process to repurpose existing commercial vendor raw genomic data for eligibility: genomic data reanalysis (GDR). Molecular results for substudy assignment were successfully generated for 369 of the first 374 patients (98.7%) using GDR for Lung-MAP, with a median time from request to result of 9 days. During the same period, 691 of 791 (87.4%) tissue samples received successfully yielded results, in a median of 14 days beyond sample acquisition. GDR is a scalable bioinformatic pipeline that expedites reanalysis of existing data for clinical trials in which validated integral biomarker testing is required for participation.
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Affiliation(s)
- Joel W Neal
- Department of Medicine, Stanford Cancer Institute, Division of Oncology, Stanford University, Palo Alto, CA, United States
| | - Katherine Minichiello
- SWOG Statistics and Data Management Center, Seattle, WA, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Ryan Brennick
- Clinical Operations, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Richard S P Huang
- Clinical Development, Foundation Medicine, Inc., Cambridge, MA, United State
| | | | - Cornel Amler
- Clinical Operations, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jyoti Patel
- Northwestern University-Feinberg School of Medicine, Chicago, IL, United States
| | - Roy Herbst
- Yale Comprehensive Cancer Center, New Haven, CT, United States
| | - Karen L Reckamp
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Hossein Borghaei
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Louise Highleyman
- SWOG Statistics and Data Management Center, Seattle, WA, United States
| | - Mary W Redman
- SWOG Statistics and Data Management Center, Seattle, WA, United States
- Clinical Research Division, Fred Hutchison Cancer Center Seattle WA, United States
| | - Lincoln W Pasquina
- Clinical Development, Foundation Medicine, Inc., Cambridge, MA, United State
| | - David E Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
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3
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Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CHG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, Reddy AT, Gupta N, Basnet KM, Macaulay RJB, Malafronte P, Lee H, Yong WH, Williams KJ, Juratli TA, Mata DA, Huang RSP, Hiemenz MC, Pavlick DC, Frampton GM, Janovitz T, Ross JS, Chang SM, Berger MS, Jacques L, Song JS, Costello JF, Solomon DA. Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs. Neuro Oncol 2023; 25:2221-2236. [PMID: 37436963 PMCID: PMC10708934 DOI: 10.1093/neuonc/noad121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Schwannomas are common peripheral nerve sheath tumors that can cause severe morbidity given their stereotypic intracranial and paraspinal locations. Similar to many solid tumors, schwannomas and other nerve sheath tumors are primarily thought to arise due to aberrant hyperactivation of the RAS growth factor signaling pathway. Here, we sought to further define the molecular pathogenesis of schwannomas. METHODS We performed comprehensive genomic profiling on a cohort of 96 human schwannomas, as well as DNA methylation profiling on a subset. Functional studies including RNA sequencing, chromatin immunoprecipitation-DNA sequencing, electrophoretic mobility shift assay, and luciferase reporter assays were performed in a fetal glial cell model following transduction with wildtype and tumor-derived mutant isoforms of SOX10. RESULTS We identified that nearly one-third of sporadic schwannomas lack alterations in known nerve sheath tumor genes and instead harbor novel recurrent in-frame insertion/deletion mutations in SOX10, which encodes a transcription factor responsible for controlling Schwann cell differentiation and myelination. SOX10 indel mutations were highly enriched in schwannomas arising from nonvestibular cranial nerves (eg facial, trigeminal, vagus) and were absent from vestibular nerve schwannomas driven by NF2 mutation. Functional studies revealed these SOX10 indel mutations have retained DNA binding capacity but impaired transactivation of glial differentiation and myelination gene programs. CONCLUSIONS We thus speculate that SOX10 indel mutations drive a unique subtype of schwannomas by impeding proper differentiation of immature Schwann cells.
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Affiliation(s)
- Erik A Williams
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Somang Kim
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jimmy Bo Yuan
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Emily Chan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Philip E LeBoit
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Thaddeus Mully
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - W Patrick Devine
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Alyssa T Reddy
- Departments of Neurology and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | | | | | | | - Han Lee
- Department of Pathology, University of California, Davis, Sacramento, California, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, California, USA
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Tareq A Juratli
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and Carl Gustav Carus University Hospital, Dresden, Germany
| | - Douglas A Mata
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | | | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | - Tyler Janovitz
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Line Jacques
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Jun S Song
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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4
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Danziger N, Sokol ES, Graf RP, Hiemenz MC, Maule J, Parimi V, Palmieri C, Pusztai L, Ross JS, Huang RSP. Variable Landscape of PD-L1 Expression in Breast Carcinoma as Detected by the DAKO 22C3 Immunohistochemistry Assay. Oncologist 2023; 28:319-326. [PMID: 36866462 PMCID: PMC10078903 DOI: 10.1093/oncolo/oyad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND In 2020, pembrolizumab was approved as a therapy for triple-negative breast cancer (TNBC) with the companion diagnostic DAKO 22C3 programmed death ligand-1 (PD-L1) immunohistochemistry assay. The study aimed to determine the landscape of PD-L1 expression as detected by the DAKO 22C3 PD-L1 assay in breast cancer subtypes and compare the clinicopathologic and genomic characteristics of PD-L1 positive and negative TNBC. METHODS PD-L1 expression using the DAKO 22C3 antibody was scored using a combined positive score (CPS) and positive status was defined as CPS ≥10. Comprehensive genomic profiling was performed using the FoundationOne CDx assay. RESULTS Of the 396 BC patients stained with DAKO 22C3, the majority were HR+/HER2- and TNBC (42% and 36%, respectively). Median PD-L1 expression and frequency of CPS ≥10 was highest in TNBC cases (median: 7.5, 50% CPS ≥10) and lowest in the HR+/HER2- group (median: 1.0, 15.5% CPS ≥10) (P < .0001). A comparison of PD-L1 positive and PD-L1 negative TNBC demonstrated no significant differences in clinicopathologic or genomic characteristics. TNBC tissue samples from the breast did have an observed enrichment for PD-L1 positivity compared to TNBC tissue samples from a metastatic site (57% vs. 44%), but this was not statistically significant (P = .1766). In the HR+/HER2- group, genomic alterations in TP53, CREBBP, and CCNE1 were more prevalent and genomic loss of heterozygosity was higher in the PD-L1(+) group compared to the PD-L1(-) group. CONCLUSIONS The subtypes of breast cancer have distinct patterns of PD-L1 expression, supporting that further research of immunotherapies may include specific evaluation of optimum cutoffs for non-TNBC patients. In TNBC, PD-L1 positivity is not associated with other clinicopathologic or genomic features and should be integrated into future studies of immunotherapy efficacy.
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Affiliation(s)
| | | | - Ryon P Graf
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Jake Maule
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Lajos Pusztai
- The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, UK
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Departments of Pathology and Urology, State University of New York Upstate Medical University, Syracuse, NY, USA
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5
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Hiemenz MC, Kaur J, Kuang Z, Huang RSP, Harries L, Metzger D, Schiavone K, Millis SZ, Lin DI, Lechpammer M, Decker B, Mata DA, Reddy A, Parke M, Lee EY, Cui X, Iwenofu OH, Buehler D, Henderson L, Baldwin E, Boikos SA, Ramkissoon SH, Smith SC. POU2AF3-rearranged Sarcomas: A Novel Tumor Defined by Fusions of EWSR1 or FUS to a Gene Formerly Designated COLCA2. Genes Chromosomes Cancer 2023. [PMID: 36862145 DOI: 10.1002/gcc.23136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/30/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023] Open
Abstract
Gene fusions involving EWSR1 or FUS as the 5' partner have been reported in a diverse array of sarcomas. Here, we characterize the histopathology and genomics of six tumors harboring a gene fusion between EWSR1 or FUS and POU2AF3, an understudied, putative colorectal cancer predisposition gene. Striking morphologic features reminiscent of synovial sarcoma were observed including a biphasic appearance with variable fusiform to epithelioid cytomorphology and staghorn-type vasculature. RNA sequencing demonstrated variable breakpoints in EWSR1/FUS along with similar breakpoints in POU2AF3 that encompassed a 3' portion of this gene. For cases in which additional information was available, the behavior of these neoplasms was aggressive with local spread and/or distant metastases. Although further studies are needed to confirm the functional significance of our findings, POU2AF3 fusions to EWSR1 or FUS may define a novel type of POU2AF3-rearranged sarcomas with aggressive, malignant behavior.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Matthew Parke
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY
| | - Xiaoyan Cui
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH
| | - O Hans Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Darya Buehler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI
| | - Erin Baldwin
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI
| | - Sosipatros A Boikos
- Division of Hematology, Oncology, and Palliative Care, Department of Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Shakti H Ramkissoon
- Foundation Medicine, Cambridge, MA.,Department of Pathology, Wake Forest School of Medicine and Wake Forest Comprehensive Cancer Center, Winston-Salem, NC
| | - Steven C Smith
- Departments of Pathology and Surgery and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA
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6
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Mata DA, Harries L, Williams EA, Hiemenz MC, Decker B, Tse JY, Janovitz T, Ferguson DC, Speece IA, Margolis ML, Mathews B, Fedorchak K, Killian JK, Xiao J, Tolba KA, Ramkissoon S, Vergilio JA, Elvin JA, Oxnard GR, Ross JS, Huang RSP. Method of Tissue Acquisition Affects Success of Comprehensive Genomic Profiling in Lung Cancer. Arch Pathol Lab Med 2023; 147:338-347. [PMID: 35771716 DOI: 10.5858/arpa.2021-0313-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Multiple procedural techniques can be used to obtain tissue to create a formalin-fixed, paraffin-embedded specimen for comprehensive genomic profiling (CGP) in lung cancer. The literature is mixed on whether the procedure affects CGP success. OBJECTIVE.— To examine whether biopsy procedure affects lung cancer CGP success. DESIGN.— This was a cross-sectional study of all patients with lung cancer whose specimens were submitted for CGP between January and February 2020. Multiple quality control metrics were used to determine whether cases were successfully profiled. RESULTS.— In all, 3312 samples were identified. Overall, 67.5% (2236 of 3312) of samples were obtained from biopsies, 13.0% (432 of 3312) from fine-needle aspirations (FNAs), 9.7% (321 of 3312) from resections, 5.3% (174 of 3312) from fluid cytology cell blocks, and 4.5% (149 of 3312) from bone biopsies. Overall, 70.1% (2321 of 3312) of cases passed CGP, 15.4% (510 of 3312) of cases were released as qualified reports, and 14.5% (481 of 3312) of cases failed CGP. Resection samples were the most likely to be successfully sequenced, failing in only 2.8% (9 of 321) of instances, while fluid cytology specimens were the least likely, failing in 23.0% (40 of 174) of instances. Biopsy (14.5% [324 of 2236]), FNA (18.5% [80 of 432]), and bone biopsy (18.8% [28 of 149]) specimens failed at intermediate frequencies. On multivariate logistic regression analysis of CGP success on specimen type, fluid cytology (odds ratio [OR], 0.08; 95% CI, 0.03-0.19), biopsy (OR, 0.25; 95% CI, 0.11-0.52), FNA (OR, 0.14; 95% CI, 0.06-0.32), and bone biopsy (OR, 0.07; 95% CI, 0.03-0.17) specimens had decreased odds of CGP success relative to resection samples. Among patients with successfully sequenced samples, 48.0% were eligible for at least 1 therapy, based on a companion diagnostic or National Comprehensive Cancer Network biomarker. CONCLUSIONS.— The method of tissue acquisition was an important preanalytic factor that determined whether a sample would be successfully sequenced and whether a clinically actionable genomic alteration would be detected.
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Affiliation(s)
| | - Lukas Harries
- From Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | | | - Julie Y Tse
- From Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | - Iain A Speece
- From Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | | | | | - Jinpeng Xiao
- From Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | | | - Julia A Elvin
- From Foundation Medicine, Inc, Cambridge, Massachusetts
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7
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Parimi V, Tolba K, Danziger N, Kuang Z, Sun D, Lin DI, Hiemenz MC, Schrock AB, Ross JS, Oxnard GR, Huang RSP. Genomic landscape of 891 RET fusions detected across diverse solid tumor types. NPJ Precis Oncol 2023; 7:10. [PMID: 36690680 PMCID: PMC9870857 DOI: 10.1038/s41698-023-00347-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
In this study, we report the clinicopathologic and genomic profiles of 891 patients with RET fusion driven advanced solid tumors. All patient samples were tested using a tissue-based DNA hybrid capture next generation sequencing (NGS) assay and a subset of the samples were liquid biopsies tested using a liquid-based hybrid capture NGS assay. RET fusions were found in 523 patients with NSCLC and in 368 patients with other solid tumors. The two tumor types with the highest number of RET fusion were lung adenocarcinoma and thyroid papillary carcinoma, and they had a prevalence rate 1.14% (455/39,922) and 9.09% (109/1199), respectively. A total of 61 novel fusions were discovered in this pan-tumor cohort. The concordance of RET fusion detection across tumor types among tissue and liquid-based NGS was 100% (8/8) in patients with greater than 1% composite tumor fraction (cTF). Herein, we present the clinicopathologic and genomic landscape of a large cohort of RET fusion positive tumors and we observed that liquid biopsy-based NGS is highly sensitive for RET fusions at cTF ≥1%.
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Affiliation(s)
- Vamsi Parimi
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Khaled Tolba
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Natalie Danziger
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Zheng Kuang
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Daokun Sun
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Douglas I. Lin
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Matthew C. Hiemenz
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Alexa B. Schrock
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
| | - Jeffrey S. Ross
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA ,grid.410412.20000 0004 0384 8998Department of Pathology and Urology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, NY USA
| | - Geoffrey R. Oxnard
- grid.418158.10000 0004 0534 4718Foundation Medicine, Inc, Cambridge, MA USA
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8
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Hiemenz MC, Graf RP, Schiavone K, Harries L, Oxnard GR, Ross JS, Huang RSP. Real-World Comprehensive Genomic Profiling Success Rates in Tissue and Liquid Prostate Carcinoma Specimens. Oncologist 2022; 27:e970-e972. [PMID: 36069892 PMCID: PMC9732218 DOI: 10.1093/oncolo/oyac181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/04/2022] [Indexed: 02/06/2023] Open
Abstract
Challenges with sequencing tissue samples from patients with prostate cancer have been reported in clinical trials. To assess the success rate of comprehensive genomic profiling (CGP) for prostate cancer patients, we analyzed a real-world cohort who underwent sequencing of their prostate tissue sample as well as a subset of patients with a reflex liquid biopsy. Overall, a significant majority (82%) of tissue prostate carcinoma samples yielded reportable CGP results. Of those samples that were unsuccessful, most (75%) were inadequate samples that did not meet pre-established criteria to advance into sequencing. For cases where liquid CGP was performed if tissue CGP was unsuccessful, mutations that were likely attributable to prostate carcinoma were observed in most cases and all cases were successful in generating a report. These results suggest that, for CGP testing, prostate cancer tissue is a reasonable matrix type and that liquid samples can be effectively used as an alternative to tissue.
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Affiliation(s)
| | - Ryon P Graf
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | | | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA,Department of Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Richard S P Huang
- Corresponding author: Richard S.P. Huang, MD, Foundation Medicine, 150 Second Street, Cambridge, MA 02141, USA.
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9
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Williams EA, Montesion M, Lincoln V, Tse JY, Hiemenz MC, Mata DA, Shah BB, Shoroye A, Alexander BM, Werth AJ, Foley-Peres K, Milante RR, Ross JS, Ramkissoon SH, Williams KJ, Adhikari LJ, Zuna RE, LeBoit PE, Lin DI, Elvin JA. HPV51-associated Leiomyosarcoma: A Novel Class of TP53/RB1-Wildtype Tumor With Predilection for the Female Lower Reproductive Tract. Am J Surg Pathol 2022; 46:729-741. [PMID: 35034043 PMCID: PMC9093731 DOI: 10.1097/pas.0000000000001862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Inactivating mutations in tumor suppressor genes TP53 and RB1 are considered central drivers in leiomyosarcomas (LMSs). In high-risk human papillomavirus (HPV)-related tumors, a similar functional outcome is achieved through oncoproteins E6 and E7, which inactivate the p53 and RB1 proteins, respectively. Here, we hypothesized that HPV infection could provide an alternative mechanism for tumorigenesis in a subset of TP53/RB1-wildtype LMS. We evaluated tumor samples from 2585 consecutive unique patients carrying a diagnosis of gynecologic or soft tissue LMS. Tumor DNA and available RNA were analyzed by hybrid-capture-based next-generation sequencing/comprehensive genomic profiling of 406 genes and transcripts (FoundationOneHeme). Of the initial 2585 cases, we excluded 16 based on the presence of molecular alterations that are considered defining for sarcomas other than LMS. In the remaining 2569 cases, we searched for LMS that were TP53/RB1-wildtype (n=486 of 2569; 18.9%). We also searched LMS tumors for HPV sequences that we then classified into genotypes by de novo assembly of nonhuman sequencing reads followed by alignment to the RefSeq database. Among TP53/RB1-wildtype LMS, we identified 18 unique cases harboring HPV sequences. Surprisingly, most (n=11) were HPV51-positive, and these 11 represented all HPV51-positive tumors in our entire LMS database (n=11 of 2569; 0.4%). The absence of genomic alterations in TP53 or RB1 in HPV51-positive LMS represented a marked difference from HPV51-negative LMS (n=2558; 0% vs. 72% [P<0.00001], 0% vs. 53% [P=0.0002]). In addition, compared with HPV51-negative LMS, HPV51-positive LMS were significantly enriched for genomic alterations in ATRX (55% vs. 24%, P=0.027) and TSC1 (18% vs. 0.6%, P=0.0047). All HPV51-positive LMS were in women; median age was 54 years at surgery (range: 23 to 74 y). All known primary sites were from the gynecologic tract or adjacent anogenital area, including 5 cases of vaginal primary site. Histology was heterogeneous, with evaluable cases showing predominant epithelioid (n=5) and spindle (n=5) morphology. In situ hybridization confirmed the presence of high-risk HPV E6/E7 mRNA in tumor cells in three of three evaluable cases harboring HPV51 genomic sequences. Overall, in our pan-LMS analysis, HPV reads were identified in a subset of TP53/RB1-wildtype LMS. For all HPV51-associated LMS, the striking absence of any detectable TP53 or RB1 mutations and predilection for the female lower reproductive tract supports our hypothesis that high-risk HPV can be an alternative tumorigenic mechanism in this distinct class of LMS.
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Affiliation(s)
- Erik A. Williams
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
- Foundation Medicine Inc., Cambridge
| | | | - Vadim Lincoln
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
| | | | | | | | | | | | | | - Adrienne J. Werth
- Department of Women’s Health Services, Hartford Hospital, Hartford, CT
| | | | - Riza R. Milante
- Department of Dermatology, Jose R. Reyes Memorial Medical Center, Manila, Philippines
| | - Jeffrey S. Ross
- Foundation Medicine Inc., Cambridge
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | - Shakti H. Ramkissoon
- Foundation Medicine Inc., Cambridge
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Laura J. Adhikari
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Rosemary E. Zuna
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Philip E. LeBoit
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
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10
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Antonarakis ES, Tierno M, Fisher V, Tukachinsky H, Alexander S, Hamdani O, Hiemenz MC, Huang RS, Oxnard GR, Graf RP. Clinical and pathological features associated with circulating tumor DNA content in real-world patients with metastatic prostate cancer. Prostate 2022; 82:867-875. [PMID: 35286728 PMCID: PMC9314037 DOI: 10.1002/pros.24331] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Liquid biopsy is a powerful tool that can enable treatment decisions for metastatic prostate cancer patients with difficult-to-biopsy tumors. However, the detection of genomic alterations via liquid biopsy is limited by the fraction (tumor fraction [TF]) of circulating tumor DNA (ctDNA) within the total cell-free DNA content. While prior work has preliminarily correlated TF with clinical features of prostate cancer, we sought to validate and provide additional resolution, such that a clinical practitioner might anticipate the probability of successful liquid biopsy profiling leveraging commonly assessed clinical and laboratory features. METHODS A total of 813 liquid biopsy specimens were assessable, with 545 associated with a PSA prostate specific antigen measurement, collected in standard-of-care settings across approximately 280 US academic or community-based cancer clinics from September 2018 to July 2021. Deidentified data were captured into a real-world clinico-genomic database (CGDB). Comprehensive genomic profiling (CGP) was performed on extracted cell-free DNA from liquid biopsy samples. RESULTS In multivariable models, higher PSA level, lower hemoglobin, lower albumin, higher alkaline phosphatase (all p < 0.001), and collection of liquid biopsy blood draw within 60 days of new treatment initiation (p = 0.002) were the most strongly associated features with higher TF. At PSA levels of <5 ng/ml, 43% of patients had a TF of <1% indicating an increased likelihood of unevaluable results. Conversely, at PSA levels of >5 ng/ml, 78% of patients had a TF of at least 1% and 46% had a TF of ≥10%, suggesting improved sensitivity for detection of targetable alterations. CONCLUSIONS Universal genomic profiling of prostate cancers will require complementary use of liquid biopsy and tumor tissue profiling for suitable patients. The likelihood of adequate ctDNA shedding into plasma is one consideration when deciding whether to pursue CGP via liquid biopsy versus tumor profiling. Our real-world data suggest that PSA < 5 ng/ml is associated with lower ctDNA yield on liquid biopsy, potentially increasing the incidence of negative results or a need for confirmation with tissue testing.
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Affiliation(s)
- Emmanuel S. Antonarakis
- Division of Hematology, Oncology and TransplantationUniversity of Minnesota, Masonic Cancer CenterMinneapolisMinnesotaUSA
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11
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Huang RSP, Tse JY, Harries L, Graf RP, Lin DI, Murugesan K, Hiemenz MC, Parimi V, Janovitz T, Decker B, Severson E, Levy MA, Ramkissoon SH, Elvin JA, Ross JS, Williams EA. OUP accepted manuscript. Oncologist 2022; 27:655-662. [PMID: 35552752 PMCID: PMC9355815 DOI: 10.1093/oncolo/oyac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
Background Materials and Methods Results Conclusions
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Affiliation(s)
- Richard S P Huang
- Corresponding author: Richard S.P. Huang, MD, 7010 Kit Creek Road, Morrisville, NC 27560, USA. Tel: +1 919 748 5944;
| | - Julie Y Tse
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Ryon P Graf
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | | | | | | | | | | | | | - Mia A Levy
- Foundation Medicine, Inc., Cambridge, MA, USA
- Rush University Medical Center, Chicago, IL, USA
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, MA, USA
- Wake Forest Comprehensive Cancer Center, and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, USA
| | - Erik A Williams
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology, Department of Dermatology, UCSF Dermatopathology Service, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, FL, USA
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12
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Huang RSP, Harries L, Decker B, Hiemenz MC, Murugesan K, Creeden J, Tolba K, Stabile LP, Ramkissoon SH, Burns TF, Ross JS. OUP accepted manuscript. Oncologist 2022; 27:839-848. [PMID: 35598205 PMCID: PMC9526503 DOI: 10.1093/oncolo/oyac094] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/31/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Richard S P Huang
- Corresponding author: Richard S.P. Huang, MD, 7010 Kit Creek Road, Morrisville, NC 27560, USA. Tel: +1 919 748 5944;
| | | | | | | | | | | | | | - Laura P Stabile
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, MA, USA
- Wake Forest Comprehensive Cancer Center, and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy F Burns
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, USA
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13
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Mirbaha H, Carrillo D, Mitui M, Hiemenz MC, Singh V, Rakheja D. Cytoplasmic P53 Immunostaining With N-Terminus P53 Antibody And Absence Of Staining With C-Terminus P53 Antibody: A Report Of Two Pediatric Sarcomas With Distal Truncating TP53 Mutations Affecting Nuclear Localization Domain. Int J Surg Pathol 2021; 30:457-461. [DOI: 10.1177/10668969211065115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
P53 immunohistochemical staining with antibodies targeted to epitopes at or near the N-terminus are commonly used in diagnostic pathology practice as a surrogate for TP53 mutations. The abnormal staining patterns indicating TP53 mutations include nuclear overexpression, null, and the recently described cytoplasmic staining. The latter staining pattern occurs with the less common TP53 mutations affecting its nuclear localization and/or tetramerization domains that are located toward the C-terminus. Here we describe the first two cases of pediatric sarcomas with cytoplasmic staining with P53 antibody against N-terminus epitope and the absence of staining with P53 antibody against C-terminus epitope. We propose that a more precise description of P53 immunohistochemical staining patterns should include the nature of the antibody used.
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Affiliation(s)
- Hilda Mirbaha
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Deyssy Carrillo
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Vivekanand Singh
- University of Texas Southwestern Medical Center, Dallas, TX, USA
- Children's Health, Dallas, TX, USA
| | - Dinesh Rakheja
- University of Texas Southwestern Medical Center, Dallas, TX, USA
- Children's Health, Dallas, TX, USA
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14
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Huang RSP, Haberberger J, McGregor K, Mata DA, Decker B, Hiemenz MC, Lechpammer M, Danziger N, Schiavone K, Creeden J, Graf RP, Strowd R, Lesser GJ, Razis ED, Bartsch R, Giannoudis A, Bhogal T, Lin NU, Pusztai L, Ross JS, Palmieri C, Ramkissoon SH. Clinicopathologic and Genomic Landscape of Breast Carcinoma Brain Metastases. Oncologist 2021; 26:835-844. [PMID: 34105210 DOI: 10.1002/onco.13855] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/28/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Among patients with breast carcinoma who have metastatic disease, 15%-30% will eventually develop brain metastases. We examined the genomic landscape of a large cohort of patients with breast carcinoma brain metastases (BCBMs) and compared it with a cohort of patients with primary breast carcinomas (BCs). MATERIAL AND METHODS We retrospectively analyzed 733 BCBMs tested with comprehensive genomic profiling (CGP) and compared them with 10,772 primary breast carcinomas (not-paired) specimens. For a subset of 16 triple-negative breast carcinoma (TNBC)-brain metastasis samples, programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) was performed concurrently. RESULTS A total of 733 consecutive BCBMs were analyzed. Compared with primary BCs, BCBMs were enriched for genomic alterations in TP53 (72.0%, 528/733), ERBB2 (25.6%, 188/733), RAD21 (14.1%, 103/733), NF1 (9.0%, 66/733), BRCA1 (7.8%, 57/733), and ESR1 (6.3%,46/733) (p < .05 for all comparisons). Immune checkpoint inhibitor biomarkers such as high tumor mutational burden (TMB-high; 16.2%, 119/733); high microsatellite instability (1.9%, 14/733); CD274 amplification (3.6%, 27/733); and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like mutational signature (5.9%, 43/733) were significantly higher in the BCBM cohort compared with the primary BC cohort (p < .05 for all comparisons). When using both CGP and PD-L1 IHC, 37.5% (6/16) of patients with TNBC brain metastasis were eligible for atezolizumab based on PD-L1 IHC, and 18.8% (3/16) were eligible for pembrolizumab based on TMB-high status. CONCLUSION We found a high prevalence of clinically relevant genomic alterations in patients with BCBM, suggesting that tissue acquisition (surgery) and/or cerebrospinal fluid for CGP in addition to CGP of the primary tumor may be clinically warranted. IMPLICATIONS FOR PRACTICE This study found a high prevalence of clinically relevant genomic alterations in patients with breast carcinoma brain metastasis (BCBM), suggesting that tissue acquisition (surgery) and/or cerebrospinal fluid for comprehensive genomic profiling (CGP) in addition to CGP of the primary tumor may be clinically warranted. In addition, this study identified higher positive rates for FDA-approved immunotherapy biomarkers detected by CGP in patients with BCBM, opening a possibility of new on-label treatments. Last, this study noted limited correlation between tumor mutational burden and PD-L1 immunohistochemistry (IHC), which shows the importance of testing patients with triple-negative BCBM for immune checkpoint inhibitor eligibility with both PD-L1 IHC and CGP.
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Affiliation(s)
| | | | | | - Douglas A Mata
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Brennan Decker
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | | | | | | | - James Creeden
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Ryon P Graf
- Foundation Medicine, Inc., San Diego, California, USA
| | - Roy Strowd
- Section on Hematology and Oncology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Glenn J Lesser
- Section on Hematology and Oncology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | | | - Athina Giannoudis
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Talvinder Bhogal
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lajos Pusztai
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,Department of Pathology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Morrisville, North Carolina, USA.,Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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15
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Huang RSP, Murugesan K, Montesion M, Pavlick DC, Mata DA, Hiemenz MC, Decker B, Frampton G, Albacker LA, Ross JS. Pan-cancer landscape of CD274 (PD-L1) copy number changes in 244 584 patient samples and the correlation with PD-L1 protein expression. J Immunother Cancer 2021; 9:e002680. [PMID: 33972391 PMCID: PMC8112409 DOI: 10.1136/jitc-2021-002680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Several studies have shown clinical outcomes data that support the use of CD274 (PD-L1) copy-number (CN) gains and/or losses as a biomarker for immune checkpoint inhibitor (ICPI). Here, we present the landscape of CD274 CN changes across a large cohort of solid tumor cases and correlate these with PD-L1 protein expression by immunohistochemistry. METHODS We analyzed all cases that underwent comprehensive genomic profiling (CGP) testing at Foundation Medicine between August 2014 and June 2020. CD274 CN changes were correlated with PD-L1 expression in tumor types where there were Food and Drug Administration approved companion diagnostic (CDx) claims and the CDx assay was used to assess PD-L1 expression. RESULTS In all, 244 584 samples representing 290 solid tumor types were included in the study. Overall, 17.6% (42 983/244 584) had CD274 CN gains (>specimen ploidy), 44.6% (108 970/244 584) were CD274 CN neutral, and 37.9% (92 631/244 584) had CD274 CN loss. Using different CN cut offs to define CD274 positivity resulted in different prevalence estimates: ploidy +1, 17.4% (42 636/244 584); ploidy +2, 6.2% (15 183/244 584); ploidy +3, 2.2% (5375/244 584); ploidy +4, 1.1% (2712/244 584); and ploidy +8, 0.2% (434/244 584). The prevalence of CN changes and CN positivity varied based on tumor type. CD274 CN gains were significantly associated with PD-L1 positivity in NSCLC, urothelial carcinoma, breast carcinoma, cervical carcinoma, esophagus squamous cell carcinoma (SCC) and head and neck SCC (ORs 3.3, 3.0, 2.0, 4.5. 3.8, 8.4, 1.4, respectively; p<0.05) and with microsatellite instability status in only clinically relevant tumor types (gastric adenocarcinoma, colorectal adenocarcinoma, uterine endometrial adenocarcinoma, esophageal adenocarcinoma and gastroesophageal junction adenocarcinoma (OR: 5.2, 1.9, 3.2, 3.7 and 6.5, respectively; p<0.05)). Conversely, CD274 CN changes were not significantly correlated with tumor mutational burden in almost all the tumor types. CONCLUSION CD274 CN changes and PD-L1 expression were highly correlated in multiple tumor types. These prevalence data on CD274 CN changes across a large cohort of different solid tumors can be used to design future clinical studies to assess whether CD274 CN changes could be a potential biomarker for ICPI.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jeffrey S Ross
- Foundation Medicine Inc, Cambridge, Massachusetts, USA
- Department of Pathology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
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16
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Ji J, Kaneva K, Hiemenz MC, Dhall G, Davidson TB, Erdreich-Epstein A, Hawes D, Hurth K, Margol AS, Mathew AJ, Robison NJ, Schmidt RJ, Tran HN, Judkins AR, Cotter JA, Biegel JA. Clinical utility of comprehensive genomic profiling in central nervous system tumors of children and young adults. Neurooncol Adv 2021; 3:vdab037. [PMID: 33948563 PMCID: PMC8080244 DOI: 10.1093/noajnl/vdab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Recent large-scale genomic studies have revealed a spectrum of genetic variants associated with specific subtypes of central nervous system (CNS) tumors. The aim of this study was to determine the clinical utility of comprehensive genomic profiling of pediatric, adolescent and young adult (AYA) CNS tumors in a prospective setting, including detection of DNA sequence variants, gene fusions, copy number alterations (CNAs), and loss of heterozygosity. Methods OncoKids, a comprehensive DNA- and RNA-based next-generation sequencing (NGS) panel, in conjunction with chromosomal microarray analysis (CMA) was employed to detect diagnostic, prognostic, and therapeutic markers. NGS was performed on 222 specimens from 212 patients. Clinical CMA data were analyzed in parallel for 66% (146/222) of cases. Results NGS demonstrated clinically significant alterations in 66% (147/222) of cases. Diagnostic markers were identified in 62% (138/222) of cases. Prognostic information and targetable genomic alterations were identified in 22% (49/222) and 18% (41/222) of cases, respectively. Diagnostic or prognostic CNAs were revealed by CMA in 69% (101/146) of cases. Importantly, clinically significant CNAs were detected in 57% (34/60) of cases with noncontributory NGS results. Germline cancer predisposition testing was indicated for 27% (57/212) of patients. Follow-up germline testing was performed for 20 patients which confirmed a germline pathogenic/likely pathogenic variant in 9 cases: TP53 (2), NF1 (2), SMARCB1 (1), NF2 (1), MSH6 (1), PMS2 (1), and a patient with 47,XXY Klinefelter syndrome. Conclusions Our results demonstrate the significant clinical utility of integrating genomic profiling into routine clinical testing for pediatric and AYA patients with CNS tumors.
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Affiliation(s)
- Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kristiyana Kaneva
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Girish Dhall
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Division of Pediatric Hematology-Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Anat Erdreich-Epstein
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kyle Hurth
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Ashley S Margol
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna J Mathew
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Nathan J Robison
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Hung N Tran
- Kaiser Permanente Los Angeles Medical Center, Los Angeles, California, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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17
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Hiemenz MC, Oberley MJ, Doan A, Aye L, Ji J, Schmidt RJ, Biegel JA, Bhojwani D, Raca G. A multimodal genomics approach to diagnostic evaluation of pediatric hematologic malignancies. Cancer Genet 2021; 254-255:25-33. [PMID: 33571894 DOI: 10.1016/j.cancergen.2021.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/24/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Detection of somatic genetic drivers is important for risk stratification and treatment selection in pediatric leukemias; however, newly recognized genetic markers may not be detected by routine karyotyping and fluorescence in situ hybridization (FISH). To identify the combination of assays that provides the highest detection rate for clinically significant molecular abnormalities, we tested 160 B- lymphoblastic leukemia (B-ALL) by karyotyping, FISH, chromosomal microarray analysis (CMA) and the custom next-generation sequencing (NGS) panel, OncoKidsⓇ. In addition, we tested 40 myeloid malignancies with karyotyping, chromosomal microarray analysis (CMA), and OncoKidsⓇ; 36/40 myeloid malignancies were also tested with FISH. In B-ALL, individual testing methods had the following diagnostic yields for the key genetic drivers: karyotype 34%; basic FISH panel 45%; FISH panel with IGH and CRLF2 probes 65%; CMA 48%; OncoKidsⓇ 39%. CMA and OncoKidsⓇ testing allowed detection of key genetic drivers in 42% of the samples that remained unknown upon testing by conventional methods. In myeloid malignancies, OncoKidsⓇ had the highest yield for detection of both primary and secondary DNA mutations and RNA fusions. Our data highlights the complementarity between CMA and NGS and conventional cytogenetics/FISH in pediatric leukemia diagnostics. Due to rapid turn-around-time, FISH may be useful as an initial screening method in B-ALL. Our data also suggests NGS testing with a comprehensive panel, despite a longer turnaround time, is a good alternative to karyotyping and FISH in pediatric AML due to its superior detection rate.
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Affiliation(s)
- Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Matthew J Oberley
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Andrew Doan
- Division of Hematology-Oncology, Children's Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Le Aye
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Deepa Bhojwani
- Division of Hematology-Oncology, Children's Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, United States; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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18
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Quindipan C, Cotter JA, Ji J, Mitchell WG, Moke DJ, Navid F, Thomas SM, VanHirtum-Das M, Wang L, Saitta SC, Biegel JA, Hiemenz MC. Custom Pediatric Oncology Next-Generation Sequencing Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care. Pediatr Neurol 2021; 114:55-59. [PMID: 33221597 DOI: 10.1016/j.pediatrneurol.2020.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/06/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Disorders in the PIK3CA-related overgrowth spectrum because of somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore archival tissue may be the only relevant available specimen for testing. Although this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders. METHODS PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing panel (OncoKids) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We used OncoKids on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by next-generation sequencing ranged from two to 13 years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention. RESULTS PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8% to 11%) than in brain (20% to 32%) and lipomatous (16% to 23%) tissues. CONCLUSIONS Our study highlights the clinical utility of using a robust, oncology-focused next-generation sequencing assay to identify PIK3CA mosaicism in noncancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis, which can then be used to improve health care management.
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Affiliation(s)
- Catherine Quindipan
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Wendy G Mitchell
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Diana J Moke
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Fariba Navid
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Stefanie M Thomas
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Michele VanHirtum-Das
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Larry Wang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Sulagna C Saitta
- Division of Medical Genets, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
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19
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Sireci AN, Patel JL, Joseph L, Hiemenz MC, Rosca OC, Caughron SK, Thibault-Sennett SA, Burke TL, Aisner DL. Molecular Pathology Economics 101: An Overview of Molecular Diagnostics Coding, Coverage, and Reimbursement: A Report of the Association for Molecular Pathology. J Mol Diagn 2020; 22:975-993. [PMID: 32504675 PMCID: PMC7267794 DOI: 10.1016/j.jmoldx.2020.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 11/26/2022] Open
Abstract
Widespread indications for use of molecular diagnostics in various aspects of clinical medicine have driven proliferation of testing. The rapid adoption and continuous technological evolution of molecular diagnostics have often strained the development and maintenance of a functional underlying framework of coding, coverage, and reimbursement policies, thereby presenting challenges to various stakeholders, including molecular professionals, payers, and patients. A multidisciplinary working group convened by the Association for Molecular Pathology Economic Affairs Committee was tasked to describe the complex landscape of molecular pathology economics and highlight opportunities for member engagement. In this article, on the basis of review and synthesis of government regulations and procedures, published payer policy documents, peer-reviewed literature, and expert consensus, the Working Group navigates the ecosystem of molecular pathology economics in terms of stakeholders, coding systems and processes, coverage policy determination, and pricing mechanisms. The composition and interrelatedness of various working groups and committees are emphasized to highlight the functional underpinnings of the system. Molecular professionals must be conversant in the language and complex inner workings of molecular pathology economics to lead successful, viable laboratories and advocate effectively for policy development on their behalf. This overview is provided to be a resource to molecular professionals as they navigate the reimbursement landscape.
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Affiliation(s)
- Anthony N Sireci
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Loxo Oncology, a wholly owned subsidiary of Eli Lilly, Stamford, Connecticut
| | - Jay L Patel
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah
| | - Loren Joseph
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Division of Clinical Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Matthew C Hiemenz
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Oana C Rosca
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Northwell Health System, Staten Island University Hospital, Staten Island, New York
| | - Samuel K Caughron
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; The MAWD Pathology Group, Lenexa, Kansas
| | | | - Tara L Burke
- Association for Molecular Pathology, Rockville, Maryland
| | - Dara L Aisner
- EAC101 Working Group, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Rockville, Maryland; Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado.
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20
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Warren M, Hiemenz MC, Schmidt R, Shows J, Cotter J, Toll S, Parham DM, Biegel JA, Mascarenhas L, Shah R. Expanding the spectrum of dicer1-associated sarcomas. Mod Pathol 2020; 33:164-174. [PMID: 31537896 PMCID: PMC7528621 DOI: 10.1038/s41379-019-0366-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 12/28/2022]
Abstract
DICER1 syndrome is a hereditary cancer predisposition syndrome caused by deleterious germline DICER1 mutations. Characteristic "hotspot" somatic mutations of DICER1 have been identified in DICER1-associated tumors. With the exception of genitourinary embryonal rhabdomyosarcoma and anaplastic sarcoma of the kidney, sarcomas are rarely reported in DICER1 syndrome. Herein, we report the clinical, histopathologic, and molecular findings of a germline DICER1-associated ovarian sarcoma in a 5-year-old female, a somatic DICER1-associated metastatic peritoneal sarcoma in a 16-year-old female, and a somatic DICER1-associated primary intracranial sarcoma in a 4-year-old male. A comprehensive review of the literature, including 83 DICER1-associated sarcomas, illustrates an unequivocal histologic pattern mimicking pleuropulmonary blastoma, regardless of the site of origin. The features include undifferentiated small round blue cells, poorly differentiated spindle cells, and large bizarre pleomorphic cells (anaplasia), often with rhabdomyoblastic and/or chondroid differentiation, and rare bone/osteoid formation. This unique heterogeneous histologic pattern should raise suspicion for pathogenic DICER1 mutation(s) warranting a detailed review of the family history and DICER1 mutation analysis. In addition to expanding the phenotypic spectrum of DICER1-associated conditions, identification of pathogenic DICER1 variants facilitates optimized genetic counseling, caregiver education and judicious imaging-based surveillance.
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Affiliation(s)
- Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Matthew C. Hiemenz
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ryan Schmidt
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jared Shows
- Department of Pathology, Long Beach Medical Center, Miller Children’s Hospital, Long Beach, CA, USA
| | - Jennifer Cotter
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephanie Toll
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David M. Parham
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaclyn A. Biegel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Leo Mascarenhas
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rachana Shah
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children’s Center for Cancer and Blood Diseases, Children’s Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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21
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Affiliation(s)
- Matthew C. Hiemenz
- Keck School of Medicine, University of Southern California, Los Angeles, CA
- Children’s Hospital Los Angeles, Los Angeles, CA
| | | | - Jennifer A. Cotter
- Keck School of Medicine, University of Southern California, Los Angeles, CA
- Children’s Hospital Los Angeles, Los Angeles, CA
| | - Jaclyn A. Biegel
- Keck School of Medicine, University of Southern California, Los Angeles, CA
- Children’s Hospital Los Angeles, Los Angeles, CA
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22
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Warren M, Anselmo D, Takeda M, Shillingford N, Hiemenz MC, Shah R. NTRK
‐rearranged mesenchymal tumour in a 3‐year‐old female: a diagnostic quandary. Histopathology 2019; 75:772-775. [DOI: 10.1111/his.13920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Mikako Warren
- Department of Pathology and Laboratory Medicine Children’s Hospital Los Angeles, Keck School of MedicineUniversity of Southern California Los AngelesCAUSA
| | - Dean Anselmo
- Division of Surgery Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California Los AngelesCAUSA
| | - Moe Takeda
- Department of Pathology and Laboratory Medicine Children’s Hospital Los Angeles, Keck School of MedicineUniversity of Southern California Los AngelesCAUSA
| | - Nick Shillingford
- Department of Pathology and Laboratory Medicine Children’s Hospital Los Angeles, Keck School of MedicineUniversity of Southern California Los AngelesCAUSA
| | - Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine Children’s Hospital Los Angeles, Keck School of MedicineUniversity of Southern California Los AngelesCAUSA
- Division of Genomic Medicine, Center for Personalized Medicine Children’s Hospital Los Angeles Los AngelesCAUSA
| | - Rachana Shah
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Children’s Center for Cancer and Blood Diseases Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California Los Angeles CA USA
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23
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Ji J, Raca G, Hiemenz MC, Maglinte DT, Bootwalla M, Lee B, Shams S, Biegel JA. 46. Evaluation of NxClinical for integration of CNV, LOH, and sequence variants for clinical cancer case review. Cancer Genet 2019. [DOI: 10.1016/j.cancergen.2019.04.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Oberley MJ, Gaynon PS, Bhojwani D, Pulsipher MA, Gardner RA, Hiemenz MC, Ji J, Han J, O’Gorman MR, Wayne AS, Raca G. Myeloid lineage switch following chimeric antigen receptor T-cell therapy in a patient with TCF3-ZNF384 fusion-positive B-lymphoblastic leukemia. Pediatr Blood Cancer 2018; 65:e27265. [PMID: 29797659 PMCID: PMC7469918 DOI: 10.1002/pbc.27265] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/27/2018] [Accepted: 05/07/2018] [Indexed: 01/09/2023]
Abstract
A pediatric patient diagnosed initially with B-lymphoblastic leukemia (B-ALL) relapsed with lineage switch to acute myeloid leukemia (AML) after chimeric antigen receptor T-cell (CAR-T) therapy and hematopoietic stem cell transplant. A TCF3-ZNF384 fusion was identified at diagnosis, persisted through B-ALL relapse, and was also present in the AML relapse cell population. ZNF384-rearrangements define a molecular subtype of B-ALL characterized by a pro-B-cell immunophenotype; furthermore, ZNF384-rearrangements are prevalent in mixed-phenotype acute leukemias. Lineage switch following CAR-T therapy has been described in patients with KMT2A (mixed lineage leukemia) rearrangements, but not previously in any patient with ZNF384 fusion.
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Affiliation(s)
- Matthew J. Oberley
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Paul S. Gaynon
- Children’s Center for Cancer and Blood Diseases and Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children’s Hospital Los Angeles, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Deepa Bhojwani
- Children’s Center for Cancer and Blood Diseases and Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children’s Hospital Los Angeles, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Michael A. Pulsipher
- Children’s Center for Cancer and Blood Diseases and Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children’s Hospital Los Angeles, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Rebecca A. Gardner
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington,Department of Pediatrics, University of Washington, Seattle, Washington
| | - Matthew C. Hiemenz
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Han
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Maurice R.G. O’Gorman
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alan S. Wayne
- Children’s Center for Cancer and Blood Diseases and Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children’s Hospital Los Angeles, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
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25
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Hiemenz MC, Ostrow DG, Busse TM, Buckley J, Maglinte DT, Bootwalla M, Done J, Ji J, Raca G, Ryutov A, Xu X, Zhen CJ, Conroy JM, Hazard FK, Deignan JL, Rogers BB, Treece AL, Parham DM, Gai X, Judkins AR, Triche TJ, Biegel JA. OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies. J Mol Diagn 2018; 20:765-776. [PMID: 30138724 DOI: 10.1016/j.jmoldx.2018.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/22/2018] [Accepted: 06/11/2018] [Indexed: 02/08/2023] Open
Abstract
The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.
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Affiliation(s)
- Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California.
| | - Dejerianne G Ostrow
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Tracy M Busse
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan Buckley
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Dennis T Maglinte
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moiz Bootwalla
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - James Done
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Alex Ryutov
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Xinjie Xu
- Cytogenetics and Genomic Microarray, ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Chao Jie Zhen
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Jeffrey M Conroy
- OmniSeq Inc., Buffalo, New York; Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Florette K Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Beverly B Rogers
- Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Amanda L Treece
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Denver, Colorado
| | - David M Parham
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Xiaowu Gai
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California
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26
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Cotter JA, Green JC, Hiemenz MC, Ji J, Biegel JA, Judkins AR. TBIO-26. INTEGRATED REPORTING FOR PEDIATRIC NEURO-ONCOLOGY: THE CHLA EXPERIENCE. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Jianling Ji
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
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27
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Moke DJ, Thomas SM, Hiemenz MC, Nael A, Wang K, Shillingford N, Biegel JA, Mascarenhas L. Three synchronous malignancies in a patient with DICER1 syndrome. Eur J Cancer 2018; 93:140-143. [PMID: 29395683 DOI: 10.1016/j.ejca.2017.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 12/21/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Diana J Moke
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Stefanie M Thomas
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Matthew C Hiemenz
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Ali Nael
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Kasper Wang
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nick Shillingford
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jaclyn A Biegel
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Leo Mascarenhas
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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28
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Fox AJ, Hiemenz MC, Lieberman DB, Sukhadia S, Li B, Grubb J, Candrea P, Ganapathy K, Zhao J, Roth D, Alley E, Loren A, Morrissette JJD. Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors. J Vis Exp 2016:52758. [PMID: 27684276 PMCID: PMC5092039 DOI: 10.3791/52758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
As our understanding of the driver mutations necessary for initiation and progression of cancers improves, we gain critical information on how specific molecular profiles of a tumor may predict responsiveness to therapeutic agents or provide knowledge about prognosis. At our institution a tumor genotyping program was established as part of routine clinical care, screening both hematologic and solid tumors for a wide spectrum of mutations using two next-generation sequencing (NGS) panels: a custom, 33 gene hematological malignancies panel for use with peripheral blood and bone marrow, and a commercially produced solid tumor panel for use with formalin-fixed paraffin-embedded tissue that targets 47 genes commonly mutated in cancer. Our workflow includes a pathologist review of the biopsy to ensure there is adequate amount of tumor for the assay followed by customized DNA extraction is performed on the specimen. Quality control of the specimen includes steps for quantity, quality and integrity and only after the extracted DNA passes these metrics an amplicon library is generated and sequenced. The resulting data is analyzed through an in-house bioinformatics pipeline and the variants are reviewed and interpreted for pathogenicity. Here we provide a snapshot of the utility of each panel using two clinical cases to provide insight into how a well-designed NGS workflow can contribute to optimizing clinical outcomes.
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Affiliation(s)
- Alan J Fox
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - David B Lieberman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Shrey Sukhadia
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Barnett Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Joseph Grubb
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Patrick Candrea
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Karthik Ganapathy
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Jianhua Zhao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - David Roth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Evan Alley
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Abramson Cancer Center
| | - Alison Loren
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Abramson Cancer Center
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania;
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29
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Hatanpaa KJ, Hu T, Vemireddy V, Foong C, Raisanen JM, Oliver D, Hiemenz MC, Burns DK, White CL, Whitworth LA, Mickey B, Stegner M, Habib AA, Fink K, Maher EA, Bachoo RM. High expression of the stem cell marker nestin is an adverse prognostic factor in WHO grade II-III astrocytomas and oligoastrocytomas. J Neurooncol 2014; 117:183-189. [PMID: 24519516 DOI: 10.1007/s11060-014-1376-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 01/19/2014] [Indexed: 12/17/2022]
Abstract
Infiltrating astrocytomas and oligoastrocytomas of low to anaplastic grade (WHO grades II and III), in spite of being associated with a wide range of clinical outcomes, can be difficult to subclassify and grade by the current histopathologic criteria. Unlike oligodendrogliomas and anaplastic oligodendrogliomas that can be identified by the 1p/19q codeletion and the more malignant glioblastomas (WHO grade IV astrocytomas) that can be diagnosed solely based on objective features on routine hematoxylin and eosin sections, no such objective criteria exist for the subclassification of grade II-III astrocytomas and oligoastrocytomas (A+OA II-III). In this study, we evaluated the prognostic and predictive value of the stem cell marker nestin in adult A+OA II-III (n = 50) using immunohistochemistry and computer-assisted analysis on tissue microarrays. In addition, the correlation between nestin mRNA level and total survival was analyzed in the NCI Rembrandt database. The results showed that high nestin expression is a strong adverse prognostic factor for total survival (p = 0.0004). The strength of the correlation was comparable to but independent of the isocitrate dehydrogenase 1/2 (IDH 1/2) mutation status. Histopathological grading and subclassification did not correlate significantly with outcome, although the interpretation of this finding is limited by the fact that grade III tumors were treated more aggressively than grade II tumors. These results suggest that nestin level and IDH 1/2 mutation status are strong prognostic features in A+OA II-III and possibly more helpful for treatment planning than routine histopathological variables such as oligodendroglial component (astrocytoma vs. oligoastrocytoma) and WHO grade (grade II vs. III).
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Affiliation(s)
- Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Tianshen Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Vamsidhara Vemireddy
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Chan Foong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jack M Raisanen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Dwight Oliver
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Matthew C Hiemenz
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Dennis K Burns
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles L White
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - L Anthony Whitworth
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bruce Mickey
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Martha Stegner
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Amyn A Habib
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX.,VA North Texas Health Care System, Dallas, TX
| | - Karen Fink
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Elizabeth A Maher
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Robert M Bachoo
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
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Hiemenz MC, Chen W, Winick N, Garcia R, Tirado CA. Coexistence of t(12;21)(p13;q22)/ETV6-RUNX1 and 11q23/MLL Rearrangement in B Acute Lymphoblastic Leukemia: A Case Report and Review of the Literature. J Assoc Genet Technol 2011; 37:213-215. [PMID: 22156147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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31
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Tirado CA, Chen W, Huang LJS, Laborde C, Hiemenz MC, Valdez F, Ho K, Winick N, Lou Z, Koduru P. Novel JAK2 rearrangement resulting from a t(9;22)(p24;q11.2) in B-acute lymphoblastic leukemia. Leuk Res 2010; 34:1674-6. [PMID: 20594592 DOI: 10.1016/j.leukres.2010.05.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 05/26/2010] [Accepted: 05/31/2010] [Indexed: 12/22/2022]
Abstract
Rearrangements of JAK2 are rare and have been described in various hematological neoplasms. We report a novel JAK2 rearrangement resulting from a t(9;22)(p24;q11.2) in a 14-year-old male with a diagnosis of B lymphoblastic leukemia. He was treated with Children's Oncology Group's protocol (AALL0232) but failed to achieve remission by day 29. He underwent a second induction and entered remission. His clinical course suggested that this JAK2 rearrangement might portend an unfavorable prognosis. This case brings the total number of JAK2 rearranged lymphoblastic leukemia cases in the literature to seven. The molecular genetic and clinicopathologic features of these cases were reviewed.
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Affiliation(s)
- Carlos A Tirado
- Department of Pathology, Clinical Cytogenetics, The University of Texas, Southwestern Medical Center at Dallas, Dallas, TX 75390-9073, USA.
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