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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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Busse TM, Roth JJ, Wilmoth D, Wainwright L, Tooke L, Biegel JA. Copy number alterations determined by single nucleotide polymorphism array testing in the clinical laboratory are indicative of gene fusions in pediatric cancer patients. Genes Chromosomes Cancer 2017; 56:730-749. [DOI: 10.1002/gcc.22477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/31/2017] [Accepted: 06/05/2017] [Indexed: 01/13/2023] Open
Affiliation(s)
- Tracy M. Busse
- Department of Pathology and Laboratory Medicine Children's Hospital of Los Angeles; Center for Personalized Medicine; Los Angeles California
| | - Jacquelyn J. Roth
- Department of Pathology and Laboratory Medicine; Hospital of the University of Pennsylvania; Philadelphia Pennsylvania
| | - Donna Wilmoth
- Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Luanne Wainwright
- Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Laura Tooke
- Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Jaclyn A. Biegel
- Department of Pathology and Laboratory Medicine Children's Hospital of Los Angeles; Center for Personalized Medicine; Los Angeles California
- Department of Pathology; USC Keck School of Medicine; Los Angeles California
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Weingart MF, Roth JJ, Hutt-Cabezas M, Busse TM, Kaur H, Price A, Maynard R, Rubens J, Taylor I, Mao XG, Xu J, Kuwahara Y, Allen SJ, Erdreich-Epstein A, Weissman BE, Orr BA, Eberhart CG, Biegel JA, Raabe EH. Disrupting LIN28 in atypical teratoid rhabdoid tumors reveals the importance of the mitogen activated protein kinase pathway as a therapeutic target. Oncotarget 2016; 6:3165-77. [PMID: 25638158 PMCID: PMC4413645 DOI: 10.18632/oncotarget.3078] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [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: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 12/26/2022] Open
Abstract
Atypical teratoid rhabdoid tumor (AT/RT) is among the most fatal of all pediatric brain tumors. Aside from loss of function mutations in the SMARCB1 (BAF47/INI1/SNF5) chromatin remodeling gene, little is known of other molecular drivers of AT/RT. LIN28A and LIN28B are stem cell factors that regulate thousands of RNAs and are expressed in aggressive cancers. We identified high-levels of LIN28A and LIN28B in AT/RT primary tumors and cell lines, with corresponding low levels of the LIN28-regulated microRNAs of the let-7 family. Knockdown of LIN28A by lentiviral shRNA in the AT/RT cell lines CHLA-06-ATRT and BT37 inhibited growth, cell proliferation and colony formation and induced apoptosis. Suppression of LIN28A in orthotopic xenograft models led to a more than doubling of median survival compared to empty vector controls (48 vs 115 days). LIN28A knockdown led to increased expression of let-7b and let-7g microRNAs and a down-regulation of KRAS mRNA. AT/RT primary tumors expressed increased mitogen activated protein (MAP) kinase pathway activity, and the MEK inhibitor selumetinib (AZD6244) decreased AT/RT growth and increased apoptosis. These data implicate LIN28/RAS/MAP kinase as key drivers of AT/RT tumorigenesis and indicate that targeting this pathway may be a therapeutic option in this aggressive pediatric malignancy.
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Affiliation(s)
- Melanie F Weingart
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jacquelyn J Roth
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marianne Hutt-Cabezas
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Tracy M Busse
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harpreet Kaur
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Antoinette Price
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Rachael Maynard
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey Rubens
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Isabella Taylor
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Xing-Gang Mao
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jingying Xu
- Division of Hematology, Oncology, and Blood & Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yasumichi Kuwahara
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Sariah J Allen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anat Erdreich-Epstein
- Division of Hematology, Oncology, and Blood & Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Eberhart
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jaclyn A Biegel
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Eric H Raabe
- Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Pediatric Oncology, Johns Hopkins University, Baltimore, MD, USA
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Betensky M, Babushok D, Roth JJ, Mason PJ, Biegel JA, Busse TM, Li Y, Lind C, Papazoglou A, Monos D, Podsakoff G, Bessler M, Olson TS. Clonal evolution and clinical significance of copy number neutral loss of heterozygosity of chromosome arm 6p in acquired aplastic anemia. Cancer Genet 2015; 209:1-10. [PMID: 26702937 DOI: 10.1016/j.cancergen.2015.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
Acquired aplastic anemia (aAA) results from the T cell-mediated autoimmune destruction of hematopoietic stem cells. Factors predicting response to immune suppression therapy (IST) or development of myelodysplastic syndrome (MDS) are beginning to be elucidated. Our recent data suggest most patients with aAA treated with IST develop clonal somatic genetic alterations in hematopoietic cells. One frequent acquired abnormality is copy-number neutral loss of heterozygosity on chromosome 6p (6p CN-LOH) involving the human leukocyte antigen (HLA) locus. We hypothesized that because 6p CN-LOH clones may arise from selective pressure to escape immune surveillance through deletion of HLA alleles, the development of 6p CN-LOH may affect response to IST. We used single nucleotide polymorphism array genotyping and targeted next-generation sequencing of HLA alleles to assess frequency of 6p CN-LOH, identity of HLA alleles lost through 6p CN-LOH, and impact of 6p CN-LOH on response to IST. 6p CN-LOH clones were present in 11.3% of patients, remained stable over time, and were not associated with development of MDS-defining cytogenetic abnormalities. Notably, no patient with 6p CN-LOH treated with IST achieved a complete response. In summary, clonal 6p CN-LOH in aAA defines a unique subgroup of patients that may provide insights into hematopoietic clonal evolution.
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Affiliation(s)
- Marisol Betensky
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daria Babushok
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jacquelyn J Roth
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Philip J Mason
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jaclyn A Biegel
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tracy M Busse
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yimei Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Curt Lind
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Papazoglou
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory Podsakoff
- Office of Clinical and Translational Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Monica Bessler
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy S Olson
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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5
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Babushok DV, Perdigones N, Perin JC, Olson TS, Ye W, Roth JJ, Lind C, Cattier C, Li Y, Hartung H, Paessler ME, Frank DM, Xie HM, Busse TM, Cross S, Podsakoff GM, Monos D, Biegel JA, Mason PJ, Bessler M. Abstract 2977: Most patients with acquired aplastic anemia develop clonal hematopoiesis early in disease. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2977] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Clonal hematopoiesis is an expansion of hematopoietic stem cells, caused by somatic mutations or epigenetic changes that confer a growth advantage to the host cell. Although recently recognized as a phenomenon of aging, clonal hematopoiesis has been traditionally associated with pre-cancerous states and malignant transformation. Acquired aplastic anemia (AA), a non-neoplastic autoimmune blood disorder occurring in children and adults, has been associated with clonal hematopoietic disorders; transformation to myelodysplastic syndrome (MDS) or acute leukemia is a late complication in 10-15% of AA patients. Based on the association of AA with clonal disorders, we hypothesized that clonal hematopoiesis is a general phenomenon in AA, and can be seen in the majority of AA patients, including children. To evaluate somatic genetic changes in AA, we used a combination of single nucleotide polymorphism array (SNP-A) genotyping and comparative whole exome sequencing of paired bone marrow aspirates and skin in twenty nine patients with AA. All somatic mutations were validated by bi-directional Sanger sequencing. The median age of diagnosis was 14 years (range 1.5-65). Patients were analyzed at a median of 1.1 years from diagnosis. None of the patients had histopathological evidence of MDS at the time of analysis. Somatic mutations were identified in the majority of patients, including patients with pediatric-onset AA. Three patients (10%) had somatic loss-of-function mutations in HLA class I alleles. Although MDS-associated mutations were identified in 2 of 29 patients, the majority of mutations were not in genes associated with MDS and hematologic malignancies. Pathway analysis of mutated genes revealed an enrichment of genes in pathways of immunity and transcriptional regulation. Comparison of somatic mutations in AA to a patient with a 30-year history of AA who progressed to MDS revealed that, unlike in AA, which was characterized by diverse and frequently oligoclonal hematopoiesis, progression to MDS was associated with an expansion of a dominant clone carrying multiple classical mutations linked to malignancy: pathogenic mutations in SUZ12 (homozygous for the mutated region due to copy number-neutral loss of heterozygosity (CN-LOH) at the chromosomal region 17q11.2qter), ASXL1, RUNX1, and PHF6. In conclusion, our data show that clonal hematopoiesis emerges in the majority of patients with AA, including children and young adults, can be detected early in disease, and has a mutational spectrum largely distinct from MDS. Our results highlight that in the absence of morphologic features of myelodysplasia, the presence of clonal hematopoiesis with somatic mutations cannot be used to distinguish MDS from AA. Future longitudinal studies of clonal hematopoiesis in AA will help to explain differences in patients’ disease course, and will enable personalized treatment approaches in AA.
Citation Format: Daria V. Babushok, Nieves Perdigones, Juan C. Perin, Timothy S. Olson, Wenda Ye, Jacquelyn J. Roth, Curt Lind, Carine Cattier, Yimei Li, Helge Hartung, Michele E. Paessler, Dale M. Frank, Hongbo M. Xie, Tracy M. Busse, Shanna Cross, Gregory M. Podsakoff, Dimitrios Monos, Jaclyn A. Biegel, Philip J. Mason, Monica Bessler. Most patients with acquired aplastic anemia develop clonal hematopoiesis early in disease. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2977. doi:10.1158/1538-7445.AM2015-2977
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Affiliation(s)
- Daria V. Babushok
- 1Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Nieves Perdigones
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Juan C. Perin
- 3Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Timothy S. Olson
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Wenda Ye
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jacquelyn J. Roth
- 4Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Curt Lind
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Carine Cattier
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yimei Li
- 6Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Helge Hartung
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Michele E. Paessler
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dale M. Frank
- 4Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Hongbo M. Xie
- 3Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tracy M. Busse
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Shanna Cross
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gregory M. Podsakoff
- 7Center for Cellular and Molecular Therapeutics, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dimitrios Monos
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jaclyn A. Biegel
- 5Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Philip J. Mason
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Monica Bessler
- 2Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
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Abstract
The identification of mutations and deletions in the SMARCB1 locus in chromosome band 22q11.2 in pediatric rhabdoid tumors provided the first evidence for the involvement of the SWI/SNF chromatin remodeling complex in cancer. Over the last 15 years, alterations in more than 20 members of the complex have been reported in a variety of human tumors. These include germline mutations and copy number alterations in SMARCB1, SMARCA4, SMARCE1, and PBRM1 that predispose carriers to both benign and malignant neoplasms. Somatic mutations, structural abnormalities, or epigenetic modifications that lead to reduced or aberrant expression of complex members have now been reported in more than 20% of malignancies, including both solid tumors and hematologic disorders in both children and adults. In this review, we will highlight the role of SMARCB1 in cancer as a paradigm for other tumors with alterations in SWI/SNF complex members and demonstrate the broad spectrum of mutations observed in complex members in different tumor types.
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Roth JJ, Santi M, Rorke-Adams LB, Harding BN, Busse TM, Tooke LS, Biegel JA. Diagnostic application of high resolution single nucleotide polymorphism array analysis for children with brain tumors. Cancer Genet 2014; 207:111-23. [PMID: 24767714 DOI: 10.1016/j.cancergen.2014.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 01/08/2014] [Revised: 03/09/2014] [Accepted: 03/10/2014] [Indexed: 12/21/2022]
Abstract
Single nucleotide polymorphism (SNP) array analysis is currently used as a first tier test for pediatric brain tumors at The Children's Hospital of Philadelphia. The results from 100 consecutive patients are summarized in the present report. Eighty-seven percent of the tumors had at least one pathogenic copy number alteration. Nineteen of 56 low grade gliomas (LGGs) demonstrated a duplication in 7q34, which resulted in a KIAA1549-BRAF fusion. Chromosome band 7q34 deletions, which resulted in a FAM131B-BRAF fusion, were identified in one pilocytic astrocytoma (PA) and one dysembryoplastic neuroepithelial tumor (DNT). One ganglioglioma (GG) demonstrated a 6q23.3q26 deletion that was predicted to result in a MYB-QKI fusion. Gains of chromosomes 5, 6, 7, 11, and 20 were seen in a subset of LGGs. Monosomy 6, deletion of 9q and 10q, and an i(17)(q10) were each detected in the medulloblastomas (MBs). Deletions and regions of loss of heterozygosity that encompassed TP53, RB1, CDKN2A/B, CHEK2, NF1, and NF2 were identified in a variety of tumors, which led to a recommendation for germline testing. A BRAF p.Thr599dup or p.V600E mutation was identified by Sanger sequencing in one and five gliomas, respectively, and a somatic TP53 mutation was identified in a fibrillary astrocytoma. No TP53 hot-spot mutations were detected in the MBs. SNP array analysis of pediatric brain tumors can be combined with pathologic examination and molecular analyses to further refine diagnoses, offer more accurate prognostic assessments, and identify patients who should be referred for cancer risk assessment.
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Affiliation(s)
- Jacquelyn J Roth
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA.
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Lucy B Rorke-Adams
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Brian N Harding
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Tracy M Busse
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Laura S Tooke
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jaclyn A Biegel
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
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