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Chang HY, Dermawan J, Sharma A, Dickson B, Turashvili G, Torrence D, Nucci M, Chiang S, Oliva E, Kirchner M, Stenzinger A, Mechtersheimer G, Antonescu C. Sarcomas With RAD51B Fusions Are Associated With a Heterogeneous Phenotype. Mod Pathol 2024; 37:100402. [PMID: 38141829 PMCID: PMC11251009 DOI: 10.1016/j.modpat.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 12/05/2023] [Indexed: 12/25/2023]
Abstract
RAD51B-rearranged sarcomas are rare neoplasms that exhibit a heterogeneous morphology. To date, 6 cases have been reported, all involving the uterus, including 4 perivascular epithelioid cell tumors (PEComas) and 2 leiomyosarcomas (LMS). In this study, we describe the morphologic, immunohistochemical, and molecular features of 8 additional sarcomas with RAD51B rearrangement, including the first extrauterine example. All patients were women with a median age of 57 years at presentation. Seven tumors originated in the uterus, and one in the lower extremity soft tissue, with a median tumor size of 12 cm. Histologically, 4 tumors showed predominantly spindle cell morphology with eosinophilic fibrillary cytoplasm, with or without nuclear pleomorphism, whereas 2 tumors exhibited pleomorphic epithelioid cells, featuring clear to eosinophilic, granular cytoplasm. Two neoplasms exhibited undifferentiated cytomorphology, including one with uniform small blue round cells. All tumors showed high-grade cytologic atypia and high mitotic activity (median: 30/10 high-power fields), whereas coagulative necrosis was noted in 6 cases and lymphovascular invasion in 2. By immunohistochemistry, 2 showed myoid and melanocytic markers in keeping with PEComa, whereas 4 cases were only positive for smooth muscle markers consistent with LMS (including 3 myxoid). The remaining 2 cases had a nonspecific immunoprofile. Five cases tested by targeted RNA sequencing (Archer FusionPlex, Illumina TruSight) showed different fusion partners (HMGA2, PDDC1, and CEP170). RAD51B rearrangements were identified by FISH in the remaining 3 cases. Targeted DNA sequencing in 2 cases was negative for TSC gene alterations. Clinical outcome, available in 5 patients (median follow-up, 19 months), revealed 3 local recurrences, 2 lung metastases, and 4 deaths due to disease. Our results expand the spectrum of sarcomas with RAD51B fusions, demonstrating variable clinical presentations, morphologic spectrum, and fusion partners. These tumors have a predilection for a uterine location, with either LMS, PEComa, or undifferentiated phenotypes, and are associated with an aggressive clinical course.
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Affiliation(s)
- Hsin-Yi Chang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Josephine Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Aarti Sharma
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brendan Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Dianne Torrence
- Department of Pathology, Northwell Health, New York, New York
| | - Marisa Nucci
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sarah Chiang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Cristina Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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2
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Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2022; 8:395-407. [PMID: 35257510 PMCID: PMC9161328 DOI: 10.1002/cjp2.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellen Cai
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Basil Horst
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Diana Ionescu
- Department of Anatomical Pathology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento, CA, USA
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Cheng Han Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Tae Hoon Lee
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Dw Twa
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Julia R Naso
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Brandon S Sheffield
- Department of Pathology and Laboratory Medicine, William Osler Health System, Brampton, ON, Canada
| | - Brian Skinnider
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tyler Smith
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellia Zhong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
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3
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Seligson ND, Tang J, Jin DX, Bennett MP, Elvin JA, Graim K, Hays JL, Millis SZ, Miles WO, Chen JL. Drivers of genomic loss of heterozygosity in leiomyosarcoma are distinct from carcinomas. NPJ Precis Oncol 2022; 6:29. [PMID: 35468996 PMCID: PMC9038792 DOI: 10.1038/s41698-022-00271-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Leiomyosarcoma (LMS) is a rare, aggressive, mesenchymal tumor. Subsets of LMS have been identified to harbor genomic alterations associated with homologous recombination deficiency (HRD); particularly alterations in BRCA2. Whereas genomic loss of heterozygosity (gLOH) has been used as a surrogate marker of HRD in other solid tumors, the prognostic or clinical value of gLOH in LMS (gLOH-LMS) remains poorly defined. We explore the genomic drivers associated with gLOH-LMS and their clinical import. Although the distribution of gLOH-LMS scores are similar to that of carcinomas, outside of BRCA2, there was no overlap with previously published gLOH-associated genes from studies in carcinomas. We note that early stage tumors with elevated gLOH demonstrated a longer disease-free interval following resection in LMS patients. Taken together, and despite similarities to carcinomas in gLOH distribution and clinical import, gLOH-LMS are driven by different genomic signals. Additional studies will be required to isolate and confirm the unique differences in biological factors driving these differences.
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Affiliation(s)
- Nathan D Seligson
- Department of Pharmacotherapy and Translational Research, The University of Florida, Jacksonville, FL, USA.,Department of Pharmacogenomics and Translational Research, Nemours Children's Specialty Care, Jacksonville, FL, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Joy Tang
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Monica P Bennett
- Department of Pharmacotherapy and Translational Research, The University of Florida, Jacksonville, FL, USA
| | | | - Kiley Graim
- Department of Computer and Information Science and Engineering, The University of Florida, Gainesville, FL, USA
| | - John L Hays
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, USA
| | | | - Wayne O Miles
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - James L Chen
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA. .,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
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A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database. Cancers (Basel) 2021; 13:cancers13174299. [PMID: 34503108 PMCID: PMC8428353 DOI: 10.3390/cancers13174299] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Glioma patients that present a somatic mutation in the isocitrate dehydrogenase 1 (IDH1) gene have a significantly better prognosis and overall survival than patients with the wild-type genotype. An IDH1 mutation is hypothesized to occur early during cellular transformation and leads to further genetic instability. A genome-wide profiling of glioma patients in the Catalogue of Somatic Mutations in Cancer (COSMIC) database was performed to classify the genetic differences in IDH1-mutant versus IDH1-wildtype patients. This classification will aid in a better understanding of how this specific mutation influences the genetic make-up of glioma and the resulting prognosis. Key differences in co-mutation and gene expression levels were identified that correlate with an improved prognosis. Abstract Gliomas are differentiated into two major disease subtypes, astrocytoma or oligodendroglioma, which are then characterized as either IDH (isocitrate dehydrogenase)-wild type or IDH-mutant due to the dramatic differences in prognosis and overall survival. Here, we investigated the genetic background of IDH1-mutant gliomas using the Catalogue of Somatic Mutations in Cancer (COSMIC) database. In astrocytoma patients, we found that IDH1 is often co-mutated with TP53, ATRX, AMBRA1, PREX1, and NOTCH1, but not CHEK2, EGFR, PTEN, or the zinc finger transcription factor ZNF429. The majority of the mutations observed in these genes were further confirmed to be either drivers or pathogenic by the Cancer-Related Analysis of Variants Toolkit (CRAVAT). Gene expression analysis showed down-regulation of DRG2 and MSN expression, both of which promote cell proliferation and invasion. There was also significant over-expression of genes such as NDRG3 and KCNB1 in IDH1-mutant astrocytoma patients. We conclude that IDH1-mutant glioma is characterized by significant genetic changes that could contribute to a better prognosis in glioma patients.
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Ansari N, Shahrabi S, Khosravi A, Shirzad R, Rezaeean H. Prognostic Significance of CHEK2 Mutation in Progression of Breast Cancer. Lab Med 2019; 50:e36-e41. [PMID: 31220302 DOI: 10.1093/labmed/lmz009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers among women; genetic mutations reflect the development of this disease. Mutations in cell signaling factors can be the main cause of BC development. In this study, we focused on mutations in checkpoint kinase 2 (CHEK2) and their impact as a prognostic factor in the pathogenesis of BC. CHEK2 is controlled in cell signaling pathways through the influence of upstream genes. Also, several downstream genes are regulated by CHEK2. In addition, mutations in CHEK2 lead to resistance of BC cells to chemotherapy and metastasis of cancer cells to other parts of the body. Finally, detection of mutations in CHEK2 can be used as a prognostic factor for patient response to treatment and for targeting downstream molecules of CHEK2 that are involved in the proliferation of breast tumor cells. Mutations such as c.1100delC and I157T can distinguish which patients are susceptible to metastasis.
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Affiliation(s)
- Narges Ansari
- Isfahan Bone Metabolic Disorders Research Center, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saeid Shahrabi
- Department of Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Abbas Khosravi
- Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Reza Shirzad
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hadi Rezaeean
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Abstract
Uterine perivascular epithelioid cell tumors (PEComas) are rare neoplasms that may show overlapping morphology and immunohistochemistry with uterine smooth muscle tumors. In this study, we evaluated the morphologic, immunohistochemical, and molecular features of 32 PEComas, including 11 with aggressive behavior. Two distinct morphologies were observed: classic (n=30) and those with a lymphangioleiomyomatosis appearance (n=2). In the former, patients ranged from 32 to 77 (mean: 51) years and 13% had tuberous sclerosis. Tumors ranged from 0.2 to 17 (mean: 5.5) cm with 77% arising in the corpus. Epithelioid cells were present in 100% and a spindled component was seen in 37%. Nuclear atypia was low (53%), intermediate (17%), or high (30%). Mitoses ranged from 0 to 36 (mean: 6) and 0 to 133 (mean: 19) per 10 and 50 high-power fields, with atypical mitoses present in 30%. Thin and delicate vessels were noted in 100%, clear/eosinophilic and granular cytoplasm in 93%, stromal hyalinization in 73%, necrosis in 30%, and lymphovascular invasion in 10%. All tumors were positive for HMB-45, cathepsin K, and at least one muscle marker, with most expressing melan-A (77%) and/or MiTF (79%). A PSF-TFE3 fusion was identified in one while another showed a RAD51B-OPHN1 fusion. Follow-up ranged from 2 to 175 (mean: 41) months, with 63% of patients alive and well, 20% dead of disease, 13% alive with disease, and 3% dead from other causes. In the latter group (n=2), patients were 39 and 49 years old, one had tuberous sclerosis, while the other had pulmonary lymphangioleiomyomatosis. Both tumors expressed HMB-45, cathepsin K, and muscle markers, but lacked TFE3 and RAD51B rearrangements. The 2 patients are currently alive and well. Application of gynecologic-specific criteria (≥4 features required for malignancy: size ≥5 cm, high-grade atypia, mitoses >1/50 high-power fields, necrosis, and lymphovascular invasion) for predicting outcome misclassified 36% (4/11) of aggressive tumors; thus, a modified algorithm with a threshold of 3 of these features is recommended to classify a PEComa as malignant.
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Chiu R, Nip KM, Chu J, Birol I. TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data. BMC Med Genomics 2018; 11:79. [PMID: 30200994 PMCID: PMC6131862 DOI: 10.1186/s12920-018-0402-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/31/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND RNA-seq is a powerful and cost-effective technology for molecular diagnostics of cancer and other diseases, and it can reach its full potential when coupled with validated clinical-grade informatics tools. Despite recent advances in long-read sequencing, transcriptome assembly of short reads remains a useful and cost-effective methodology for unveiling transcript-level rearrangements and novel isoforms. One of the major concerns for adopting the proven de novo assembly approach for RNA-seq data in clinical settings has been the analysis turnaround time. To address this concern, we have developed a targeted approach to expedite assembly and analysis of RNA-seq data. RESULTS Here we present our Targeted Assembly Pipeline (TAP), which consists of four stages: 1) alignment-free gene-level classification of RNA-seq reads using BioBloomTools, 2) de novo assembly of individual targets using Trans-ABySS, 3) alignment of assembled contigs to the reference genome and transcriptome with GMAP and BWA and 4) structural and splicing variant detection using PAVFinder. We show that PAVFinder is a robust gene fusion detection tool when compared to established methods such as Tophat-Fusion and deFuse on simulated data of 448 events. Using the Leucegene acute myeloid leukemia (AML) RNA-seq data and a set of 580 COSMIC target genes, TAP identified a wide range of hallmark molecular anomalies including gene fusions, tandem duplications, insertions and deletions in agreement with published literature results. Moreover, also in this dataset, TAP captured AML-specific splicing variants such as skipped exons and novel splice sites reported in studies elsewhere. Running time of TAP on 100-150 million read pairs and a 580-gene set is one to 2 hours on a 48-core machine. CONCLUSIONS We demonstrated that TAP is a fast and robust RNA-seq variant detection pipeline that is potentially amenable to clinical applications. TAP is available at http://www.bcgsc.ca/platform/bioinfo/software/pavfinder.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
| | - Justin Chu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada. .,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
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8
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Thibodeau ML, Bonakdar M, Zhao E, Mungall KL, Reisle C, Zhang W, Bye MH, Thiessen N, Bleile D, Mungall AJ, Ma YP, Jones MR, Renouf DJ, Lim HJ, Yip S, Ng T, Ho C, Laskin J, Marra MA, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol 2018; 2:8. [PMID: 29872726 PMCID: PMC5871832 DOI: 10.1038/s41698-018-0050-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
Eccrine porocarcinomas (EPs) are rare malignant tumours of the intraepidermic sweat gland duct and most often arise from benign eccrine poromas. Some recurrent somatic genomic events have been identified in these malignancies, but very little is known about the complexity of their molecular pathophysiology. We describe the whole genome and whole transcriptome genomic profiling of a metastatic EP in a 66-year-old male patient with a previous history of localized porocarcinoma of the scalp. Whole genome and whole transcriptome genomic profiling was performed on the metastatic EP. Whole genome sequencing was performed on blood-derived DNA in order to allow a comparison between germline and somatic events. We found somatic copy losses of several tumour suppressor genes including APC, PTEN and CDKN2A, CDKN2B and CDKN1A. We identified a somatic hemizygous CDKN2A pathogenic splice site variant. De novo transcriptome assembly revealed abnormal splicing of CDKN2A p14ARF and p16INK4a. Elevated expression of oncogenes EGFR and NOTCH1 was noted and no somatic mutations were found in these genes. Wnt pathway somatic alterations were also observed. In conclusion, our results suggest that the molecular pathophysiology of malignant EP features high complexity and subtle interactions of multiple key genes. Cell cycle dysregulation and CDKN2A loss of function was found to be a new potential driver in EP tumourigenesis. Moreover, the combination of somatic copy number variants and abnormal gene expression perhaps partly related to epigenetic mechanisms, all likely contribute to the development of this rare malignancy in our patient.
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Melika Bonakdar
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Eric Zhao
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Karen L. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Caralyn Reisle
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Wei Zhang
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Morgan H. Bye
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Nina Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Dustin Bleile
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Yussanne P. Ma
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Martin R. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Daniel J. Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Howard J. Lim
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Tony Ng
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Cheryl Ho
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Janessa Laskin
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Marco A. Marra
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Kasmintan A. Schrader
- Hereditary Cancer Program, Department of Medical Genetics, British Columbia Cancer Agency, 614–750 West Broadway, Vancouver, BC V5Z 1H5 Canada
| | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
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