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Macke EL, Miller AR, Stonerock E, Olshefski R, Zajo K, Bedrosian TA, Mardis ER, Akkari YMN, Cottrell CE, Schieffer KM. A LINE-1 mediated deletion resulting in germline retinoblastoma predisposition. Neurooncol Adv 2024; 6:vdad163. [PMID: 38213835 PMCID: PMC10783486 DOI: 10.1093/noajnl/vdad163] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Retinoblastoma is an ocular cancer associated with genomic variation in the RB1 gene. In individuals with bilateral retinoblastoma, a germline variant in RB1 is identified in virtually all cases. We describe herein an individual with bilateral retinoblastoma for whom multiple clinical lab assays performed by outside commercial laboratories failed to identify a germline RB1 variant. Paired tumor/normal exome sequencing, long-read whole genome sequencing, and long-read isoform sequencing was performed on a translational research basis ultimately identified a germline likely de novo Long Interspersed Nuclear Element (LINE)-1 mediated deletion resulting in a premature stop of translation of RB1 as the underlying genetic cause of retinoblastoma in this individual. Based on these research findings, the LINE-1 mediated deletion was confirmed via Sanger sequencing in our clinical laboratory, and results were reported in the patient's medical record to allow for appropriate genetic counseling.
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Affiliation(s)
- Erica L Macke
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Randal Olshefski
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kristin Zajo
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Yassmine M N Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
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2
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Schieffer KM, Moccia A, Bucknor BA, Stonerock E, Jayaraman V, Jenkins H, McKinney A, Koo SC, Mathew MT, Mardis ER, Lee K, Reshmi SC, Cottrell CE. Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements. Cancers (Basel) 2023; 15:4394. [PMID: 37686670 PMCID: PMC10486946 DOI: 10.3390/cancers15174394] [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: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.
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Affiliation(s)
- Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Amanda Moccia
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Brianna A. Bucknor
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Heather Jenkins
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Selene C. Koo
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Mariam T. Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Shalini C. Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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3
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Koo SC, Schieffer KM, Lee K, Gupta A, Pfau RB, Avenarius MR, Stonerock E, LaHaye S, Fitch J, Setty BA, Roberts R, Ranalli M, Conces MR, Bu F, Mardis ER, Cottrell CE. EGFR internal tandem duplications in fusion-negative congenital and neonatal spindle cell tumors. Genes Chromosomes Cancer 2023; 62:17-26. [PMID: 35801295 DOI: 10.1002/gcc.23087] [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: 04/25/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) assays can sensitively detect somatic variation, and increasingly can enable the identification of complex structural rearrangements. A subset of infantile spindle cell sarcomas, particularly congenital mesoblastic nephromas with classic or mixed histology, have structural rearrangement in the form of internal tandem duplications (ITD) involving EGFR. We performed prospective analysis to identify EGFR ITD through clinical or research studies, as well as retrospective analysis to quantify the frequency of EGFR ITD in pediatric sarcomas. Within our institution, three tumors with EGFR ITD were prospectively identified, all occurring in patients less than 1 year of age at diagnosis, including two renal tumors and one mediastinal soft tissue tumor. These three cases exhibited both cellular and mixed cellular and classic histology. All patients had no evidence of disease progression off therapy, despite incomplete resection. To extend our analysis and quantify the frequency of EGFR ITD in pediatric sarcomas, we retrospectively analyzed a cohort of tumors (n = 90) that were previously negative for clinical RT-PCR-based fusion testing. We identified EGFR ITD in three analyzed cases, all in patients less than 1 year of age (n = 18; 3/18, 17%). Here we expand the spectrum of tumors with EGFR ITD to congenital soft tissue tumors and report an unusual example of an EGFR ITD in a tumor with cellular congenital mesoblastic nephroma histology. We also highlight the importance of appropriate test selection and bioinformatic analysis for identification of this genomic alteration that is unexpectedly common in congenital and infantile spindle cell tumors.
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Affiliation(s)
- Selene C Koo
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristy Lee
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Ajay Gupta
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ruthann B Pfau
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bhuvana A Setty
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ryan Roberts
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mark Ranalli
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Miriam R Conces
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Fang Bu
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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4
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Logan SJ, Schieffer KM, Conces MR, Stonerock E, Miller AR, Fitch J, LaHaye S, Voytovich K, McGrath S, Magrini V, White P, Wilson RK, Mardis ER, Cottrell CE, Koo SC. Novel morphologic findings in PLAG1-rearranged soft tissue tumors. Genes Chromosomes Cancer 2021; 60:577-585. [PMID: 33893698 DOI: 10.1002/gcc.22953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 12/13/2022] Open
Abstract
Oncogenesis in PLAG1-rearranged tumors often results from PLAG1 transcription factor overexpression driven by promoter-swapping between constitutively expressed fusion partners. PLAG1-rearranged tumors demonstrate diverse morphologies. This study adds to this morphologic heterogeneity by introducing two tumors with PLAG1 rearrangements that display distinct histologic features. The first arose in the inguinal region of a 3-year-old, appeared well-circumscribed with a multinodular pattern, and harbored two fusions: ZFHX4-PLAG1 and CHCHD7-PLAG1. The second arose in the pelvic cavity of a 15-year-old girl, was extensively infiltrative and vascularized with an adipocytic component, and demonstrated a COL3A1-PLAG1 fusion. Both showed low-grade cytomorphology, scarce mitoses, no necrosis, and expression of CD34 and desmin. The ZFHX4-/CHCHD7-PLAG1-rearranged tumor showed no evidence of recurrence after 5 months. By contrast, the COL3A1-PLAG1-rearranged tumor quickly recurred following primary excision with positive margins; subsequent re-excision with adjuvant chemotherapy resulted in no evidence of recurrence after 2 years. While both tumors show overlap with benign and malignant fibroblastic and fibrovascular neoplasms, they also display divergent features. These cases highlight the importance of appropriate characterization in soft tissue tumors with unusual clinical and histologic characteristics.
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Affiliation(s)
- Suzanna J Logan
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Miriam R Conces
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kyle Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Sean McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Selene C Koo
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
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5
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Carroll AJ, Shago M, Mikhail FM, Raimondi SC, Hirsch BA, Loh ML, Raetz EA, Borowitz MJ, Wood BL, Maloney KW, Mattano LA, Larsen EC, Gastier-Foster J, Stonerock E, Ell D, Kahwash S, Devidas M, Harvey RC, Chen IML, Willman CL, Hunger SP, Winick NJ, Carroll WL, Rao KW, Heerema NA. Masked hypodiploidy: Hypodiploid acute lymphoblastic leukemia (ALL) mimicking hyperdiploid ALL in children: A report from the Children's Oncology Group. Cancer Genet 2019; 238:62-68. [PMID: 31425927 DOI: 10.1016/j.cancergen.2019.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 03/26/2019] [Revised: 06/28/2019] [Accepted: 07/27/2019] [Indexed: 10/26/2022]
Abstract
Hyperdiploidy with greater than 50 chromosomes is usually associated with favorable prognosis in pediatric acute lymphoblastic leukemia (ALL), whereas hypodiploidy with ≤43 chromosomes is associated with extremely poor prognosis. Sometimes, hypodiploidy is "masked" and patients do not have a karyotypically visible clone with ≤43 chromosomes. Instead, their abnormal karyotypes contain 50-78 or more chromosomes from doubling of previously hypodiploid cells. When the hypodiploid and doubled hyperdiploid clones are both present, patients can be identified by traditional test methods [karyotype, DNA Index (DI), fluorescence in situ hybridization (FISH)], but the incidence of masked hypodiploid cases in which only the doubled clone is visible is unknown. We analyzed 7013 patients with B-ALL enrolled in COG AALL03B1 (2003-2011) for whom chromosome studies were available. Of 115 patients with hypodiploidy (25-39 chromosomes), karyotypes of 40 showed only the hypodiploid clone, 47 showed mosaicism with both hypodiploid and hyperdiploid (doubled) karyotypes, and 28 with masked hypodiploidy showed only a hyperdiploid (doubled) clone. Unique karyotypic signatures were identified, and widespread loss of heterozygosity (LOH) was seen in the microsatellite panel for all patients with masked hypodiploidy. An increased awareness of the unusual karyotypic profile associated with a doubled hypodiploid clone and coordinated use of DI, FISH, and LOH studies when indicated can identify patients with masked hypodiploidy and allow appropriate treatment selection.
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Affiliation(s)
- Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Mary Shago
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Susana C Raimondi
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Betsy A Hirsch
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mignon L Loh
- Department of Pediatrics, UCSF Medical Center-Mission Bay, San Francisco, CA, USA
| | - Elizabeth A Raetz
- Department of Pediatrics, New York University Medical Center, New York, NY, USA
| | - Michael J Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Brent L Wood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Eric C Larsen
- Maine Children's Cancer Program, Scarborough, ME, USA
| | - Julie Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Eileen Stonerock
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Denise Ell
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Samir Kahwash
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Meenakshi Devidas
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | | | - I-Ming L Chen
- University of New Mexico Cancer Center, Albuquerque, NM, USA
| | | | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naomi J Winick
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William L Carroll
- Department of Pediatrics, New York University Medical Center, New York, NY, USA
| | - Kathleen W Rao
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, OH, USA
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6
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Gu Z, Churchman M, Roberts K, Li Y, Liu Y, Harvey RC, McCastlain K, Reshmi SC, Payne-Turner D, Iacobucci I, Shao Y, Chen IM, Valentine M, Pei D, Mungall KL, Mungall AJ, Ma Y, Moore R, Marra M, Stonerock E, Gastier-Foster JM, Devidas M, Dai Y, Wood B, Borowitz M, Larsen EE, Maloney K, Mattano Jr LA, Angiolillo A, Salzer WL, Burke MJ, Gianni F, Spinelli O, Radich JP, Minden MD, Moorman AV, Patel B, Fielding AK, Rowe JM, Luger SM, Bhatia R, Aldoss I, Forman SJ, Kohlschmidt J, Mrózek K, Marcucci G, Bloomfield CD, Stock W, Kornblau S, Kantarjian HM, Konopleva M, Paietta E, Willman CL, L. Loh M, P. Hunger S, Mullighan CG. Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia. Nat Commun 2016; 7:13331. [PMID: 27824051 PMCID: PMC5105166 DOI: 10.1038/ncomms13331] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022] Open
Abstract
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2D-BCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5.3% of cases lacking recurring alterations. MEF2D-rearranged ALL is characterized by a distinct immunophenotype, DNA copy number alterations at the rearrangement sites, older diagnosis age and poor outcome. The rearrangements result in enhanced MEF2D transcriptional activity, lymphoid transformation, activation of HDAC9 expression and sensitive to histone deacetylase inhibitor treatment. Thus, MEF2D-rearranged ALL represents a distinct form of high-risk leukaemia, for which new therapeutic approaches should be considered.
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Affiliation(s)
- Zhaohui Gu
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Michelle Churchman
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Kathryn Roberts
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Yongjin Li
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yu Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard C. Harvey
- University of New Mexico Cancer Center, Albuquerque, New Mexico 87106, USA
| | - Kelly McCastlain
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Shalini C. Reshmi
- The Research Institute, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Debbie Payne-Turner
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Ilaria Iacobucci
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
| | - Ying Shao
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - I-Ming Chen
- University of New Mexico Cancer Center, Albuquerque, New Mexico 87106, USA
| | - Marcus Valentine
- Cytogenetic Shared Resource, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Deqing Pei
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Karen L. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Eileen Stonerock
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Julie M. Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Meenakshi Devidas
- Department of Biostatistics, Colleges of Medicine and Public Health & Health Professions, University of Florida, Gainesville, Florida 32611, USA
| | - Yunfeng Dai
- Department of Biostatistics, Colleges of Medicine and Public Health & Health Professions, University of Florida, Gainesville, Florida 32611, USA
| | - Brent Wood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Michael Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21287, USA
| | - Eric E. Larsen
- Maine Children's Cancer Program, Scarborough, Maine 04074, USA
| | - Kelly Maloney
- Pediatric Hematology/Oncology/BMT, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado 80045, USA
| | | | - Anne Angiolillo
- Children's National Medical Center, Washington, DC 20010, USA
| | - Wanda L. Salzer
- US Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, USA
| | | | - Francesca Gianni
- Department of Hematology and Bone Marrow Transplantation, Papa Giovanni XXIII Hospital Piazza OMS 1 24127, Bergamo, Italy
| | - Orietta Spinelli
- Department of Hematology and Bone Marrow Transplantation, Papa Giovanni XXIII Hospital Piazza OMS 1 24127, Bergamo, Italy
| | - Jerald P. Radich
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Anthony V. Moorman
- Leukemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bella Patel
- Department of Haemato-Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | | | - Jacob M. Rowe
- Hematology, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Selina M. Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Bhatia
- Division of Hematology and Oncology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Ibrahim Aldoss
- Division of Hematology and Oncology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Stephen J. Forman
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, California 91010, USA
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
- Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, California 91010, USA
| | - Clara D. Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Wendy Stock
- University of Chicago Medical Center, Chicago, Illinois 60637, USA
| | - Steven Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hagop M. Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Elisabeth Paietta
- Cancer Center, Montefiore Medical Center North Division, Bronx, New York 10467, USA
| | - Cheryl L. Willman
- University of New Mexico Cancer Center, Albuquerque, New Mexico 87106, USA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children's Hospital, San Francisco, California 94158, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California 94115, USA
| | - Stephen P. Hunger
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Charles G. Mullighan
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, 262 Danny Thomas Place, MS 342, Memphis, Tennessee 38105, USA
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7
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Kalman L, Leonard J, Gerry N, Tarleton J, Bridges C, Gastier-Foster JM, Pyatt RE, Stonerock E, Johnson MA, Richards CS, Schrijver I, Ma T, Miller VR, Adadevoh Y, Furlong P, Beiswanger C, Toji L. Quality assurance for Duchenne and Becker muscular dystrophy genetic testing: development of a genomic DNA reference material panel. J Mol Diagn 2011; 13:167-74. [PMID: 21354051 DOI: 10.1016/j.jmoldx.2010.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/29/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are allelic X-linked recessive disorders that affect approximately 1 in 3500 and 1 in 20,000 male individuals, respectively. Approximately 65% of patients with DMD have deletions, 7% to 10% have duplications, and 25% to 30% have point mutations in one or more of the 79 exons of the dystrophin gene. Most clinical genetics laboratories test for deletions, and some use technologies that can detect smaller mutations and duplications. Reference and quality control materials for DMD/BMD diagnostic and carrier genetic testing are not commercially available. To help address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing and the DMD/BMD patient communities and the Coriell Cell Repositories, have characterized new and existing cell lines to create a comprehensive DMD/BMD reference material panel. Samples from 31 Coriell DMD cell lines from male probands and female carriers were analyzed using the Affymetrix SNP Array 6.0 and Multiplex Ligation-Dependent Probe Amplification (MRC-Holland BV, Amsterdam, the Netherlands), a multiplex PCR assay, and DNA sequence analysis. Identified were 16 cell lines with deletions, 9 with duplications, and 4 with point mutations distributed throughout the dystrophin gene. There were no discordant results within assay limitations. These samples are publicly available from Coriell Institute for Medical Research (Camden, NJ) and can be used for quality assurance, proficiency testing, test development, and research, and should help improve the accuracy of DMD testing.
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Affiliation(s)
- Lisa Kalman
- Division of Laboratory Science and Standards, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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