1
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Byrne AB, Arts P, Ha TT, Kassahn KS, Pais LS, O'Donnell-Luria A, Babic M, Frank MSB, Feng J, Wang P, Lawrence DM, Eshraghi L, Arriola L, Toubia J, Nguyen H, McGillivray G, Pinner J, McKenzie F, Morrow R, Lipsett J, Manton N, Khong TY, Moore L, Liebelt JE, Schreiber AW, King-Smith SL, Hardy TSE, Jackson MR, Barnett CP, Scott HS. Author Correction: Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death. Nat Med 2024; 30:302. [PMID: 37429925 DOI: 10.1038/s41591-023-02487-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Affiliation(s)
- Alicia B Byrne
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong T Ha
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Karin S Kassahn
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Lynn S Pais
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O'Donnell-Luria
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Childrens Hospital, Boston, MA, USA
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Mahalia S B Frank
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Jinghua Feng
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Paul Wang
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - David M Lawrence
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Leila Eshraghi
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Luis Arriola
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - John Toubia
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Hung Nguyen
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute and Royal Women's Hospital, Melbourne, Victoria, Australia
| | - Jason Pinner
- Centre for Clinical Genetics, Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- School of Women's and Children's Health, University of NSW, Sydney, New South Wales, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, Perth, Western Australia, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Rebecca Morrow
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- Department of Anatomical Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Jill Lipsett
- Department of Anatomical Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Nick Manton
- Department of Anatomical Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - T Yee Khong
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Anatomical Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Lynette Moore
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Anatomical Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Jan E Liebelt
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Repromed, Dulwich, South Australia, Australia
| | - Andreas W Schreiber
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Sarah L King-Smith
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- Australian Genomics, Parkville, Victoria, Australia
| | - Tristan S E Hardy
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Repromed, Dulwich, South Australia, Australia
| | - Matilda R Jackson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
- Australian Genomics, Parkville, Victoria, Australia
| | - Christopher P Barnett
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia.
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia.
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
- ACRF Genomics Facility, Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.
- Australian Genomics, Parkville, Victoria, Australia.
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2
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Homan CC, Drazer MW, Yu K, Lawrence DM, Feng J, Arriola-Martinez L, Pozsgai MJ, McNeely KE, Ha T, Venugopal P, Arts P, King-Smith SL, Cheah J, Armstrong M, Wang P, Bödör C, Cantor AB, Cazzola M, Degelman E, DiNardo CD, Duployez N, Favier R, Fröhling S, Rio-Machin A, Klco JM, Krämer A, Kurokawa M, Lee J, Malcovati L, Morgan NV, Natsoulis G, Owen C, Patel KP, Preudhomme C, Raslova H, Rienhoff H, Ripperger T, Schulte R, Tawana K, Velloso E, Yan B, Kim E, Sood R, Hsu AP, Holland SM, Phillips K, Poplawski NK, Babic M, Wei AH, Forsyth C, Mar Fan H, Lewis ID, Cooney J, Susman R, Fox LC, Blombery P, Singhal D, Hiwase D, Phipson B, Schreiber AW, Hahn CN, Scott HS, Liu P, Godley LA, Brown AL. Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41. Blood Adv 2023; 7:6092-6107. [PMID: 37406166 PMCID: PMC10582382 DOI: 10.1182/bloodadvances.2023010045] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/22/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Individuals with germ line variants associated with hereditary hematopoietic malignancies (HHMs) have a highly variable risk for leukemogenesis. Gaps in our understanding of premalignant states in HHMs have hampered efforts to design effective clinical surveillance programs, provide personalized preemptive treatments, and inform appropriate counseling for patients. We used the largest known comparative international cohort of germline RUNX1, GATA2, or DDX41 variant carriers without and with hematopoietic malignancies (HMs) to identify patterns of genetic drivers that are unique to each HHM syndrome before and after leukemogenesis. These patterns included striking heterogeneity in rates of early-onset clonal hematopoiesis (CH), with a high prevalence of CH in RUNX1 and GATA2 variant carriers who did not have malignancies (carriers-without HM). We observed a paucity of CH in DDX41 carriers-without HM. In RUNX1 carriers-without HM with CH, we detected variants in TET2, PHF6, and, most frequently, BCOR. These genes were recurrently mutated in RUNX1-driven malignancies, suggesting CH is a direct precursor to malignancy in RUNX1-driven HHMs. Leukemogenesis in RUNX1 and DDX41 carriers was often driven by second hits in RUNX1 and DDX41, respectively. This study may inform the development of HHM-specific clinical trials and gene-specific approaches to clinical monitoring. For example, trials investigating the potential benefits of monitoring DDX41 carriers-without HM for low-frequency second hits in DDX41 may now be beneficial. Similarly, trials monitoring carriers-without HM with RUNX1 germ line variants for the acquisition of somatic variants in BCOR, PHF6, and TET2 and second hits in RUNX1 are warranted.
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Affiliation(s)
- Claire C. Homan
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Michael W. Drazer
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Kai Yu
- Division of Intramural Research, Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - David M. Lawrence
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Jinghua Feng
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Luis Arriola-Martinez
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Matthew J. Pozsgai
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Kelsey E. McNeely
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Parvathy Venugopal
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Sarah L. King-Smith
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Jesse Cheah
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Mark Armstrong
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Paul Wang
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Alan B. Cantor
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Erin Degelman
- Alberta Children’s Hospital, Calgary, Alberta, Canada
| | - Courtney D. DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicolas Duployez
- Laboratory of Hematology, Biology and Pathology Center, Centre Hospitalier Regional Universitaire de Lille, Lille, France
- Jean-Pierre Aubert Research Center, INSERM, Universitaire de Lille, Lille, France
| | - Remi Favier
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Children's Hospital, Paris, France
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ana Rio-Machin
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | | | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Mineo Kurokawa
- Department of Hematology & Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Joanne Lee
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Neil V. Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Carolyn Owen
- Division of Hematology and Hematological Malignancies, Foothills Medical Centre, Calgary, AB, Canada
| | - Keyur P. Patel
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Claude Preudhomme
- Laboratory of Hematology, Biology and Pathology Center, Centre Hospitalier Regional Universitaire de Lille, Lille, France
- Jean-Pierre Aubert Research Center, INSERM, Universitaire de Lille, Lille, France
| | - Hana Raslova
- Institut Gustave Roussy, Université Paris Sud, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Villejuif, France
| | | | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Rachael Schulte
- Division of Pediatric Hematology and Oncology, Riley Children’s Hospital, Indiana University School of Medicine, Indianapolis, IN
| | - Kiran Tawana
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Elvira Velloso
- Service of Hematology, Transfusion and Cell Therapy and Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31) HCFMUSP, University of Sao Paulo Medical School, Sao Paulo, Brazil
- Genetics Laboratory, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Benedict Yan
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Erika Kim
- National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Raman Sood
- Division of Intramural Research, Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Amy P. Hsu
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M. Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kerry Phillips
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicola K. Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Andrew H. Wei
- Department of Haematology, Peter McCallum Cancer Centre, Royal Melbourne Hospital, Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Cecily Forsyth
- Central Coast Haematology, North Gosford, NSW, Australia
| | - Helen Mar Fan
- Department of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ian D. Lewis
- Adelaide Oncology & Haematology, North Adelaide, SA, Australia
| | - Julian Cooney
- Department of Haematology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia
| | - Lucy C. Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Deepak Singhal
- Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Devendra Hiwase
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Belinda Phipson
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Paediatrics and Department of Molecular Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Andreas W. Schreiber
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Paul Liu
- Division of Intramural Research, Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Lucy A. Godley
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Anna L. Brown
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
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3
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Shanmuganathan N, Wadham C, Shahrin N, Feng J, Thomson D, Wang P, Saunders V, Kok CH, King RM, Kenyon RR, Lin M, Pagani IS, Ross DM, Yong ASM, Grigg AP, Mills AK, Schwarer AP, Braley J, Altamura H, Yeung DT, Scott HS, Schreiber AW, Hughes TP, Branford S. Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention. Haematologica 2023; 108:2380-2395. [PMID: 36951160 PMCID: PMC10483360 DOI: 10.3324/haematol.2022.282184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The BCR::ABL1 gene fusion initiates chronic myeloid leukemia (CML); however, evidence has accumulated from studies of highly selected cohorts that variants in other cancer-related genes are associated with treatment failure. Nevertheless, the true incidence and impact of additional genetic abnormalities (AGA) at diagnosis of chronic phase (CP)-CML is unknown. We sought to determine whether AGA at diagnosis in a consecutive imatinib-treated cohort of 210 patients enrolled in the TIDEL-II trial influenced outcome despite a highly proactive treatment intervention strategy. Survival outcomes including overall survival, progression-free survival, failure-free survival, and BCR::ABL1 kinase domain mutation acquisition were evaluated. Molecular outcomes were measured at a central laboratory and included major molecular response (MMR, BCR::ABL1 ≤0.1%IS), MR4 (BCR::ABL1 ≤0.01%IS), and MR4.5 (BCR::ABL1 ≤0.0032%IS). AGA included variants in known cancer genes and novel rearrangements involving the formation of the Philadelphia chromosome. Clinical outcomes and molecular response were assessed based on the patient's genetic profile and other baseline factors. AGA were identified in 31% of patients. Potentially pathogenic variants in cancer-related genes were detected in 16% of patients at diagnosis (including gene fusions and deletions) and structural rearrangements involving the Philadelphia chromosome (Ph-associated rearrangements) were detected in 18%. Multivariable analysis demonstrated that the combined genetic abnormalities plus the EUTOS long-term survival clinical risk score were independent predictors of lower molecular response rates and higher treatment failure. Despite a highly proactive treatment intervention strategy, first-line imatinib-treated patients with AGA had poorer response rates. These data provide evidence for the incorporation of genomically-based risk assessment for CML.
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MESH Headings
- Humans
- Imatinib Mesylate/therapeutic use
- Antineoplastic Agents/therapeutic use
- Philadelphia Chromosome
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myeloid, Chronic-Phase/drug therapy
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG).
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide
| | - NurHezrin Shahrin
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Jinghua Feng
- Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Daniel Thomson
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Paul Wang
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Verity Saunders
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide
| | - Chung Hoow Kok
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
| | - Rob M King
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Rosalie R Kenyon
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ming Lin
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ilaria S Pagani
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - David M Ross
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Flinders University and Medical Centre, Adelaide
| | - Agnes S M Yong
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); The University of Western Australia Medical School, Western Australia
| | - Andrew P Grigg
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Clinical Hematology, Austin Hospital and University of Melbourne, Melbourne
| | - Anthony K Mills
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Princess Alexandra Hospital, Brisbane
| | - Anthony P Schwarer
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Box Hill Hospital, Melbourne
| | - Jodi Braley
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - Haley Altamura
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - David T Yeung
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia; School of Biological Sciences, University of Adelaide, Adelaide
| | - Timothy P Hughes
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Susan Branford
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
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4
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Samaraweera SE, Geukens T, Casolari DA, Nguyen T, Sun C, Bailey S, Moore S, Feng J, Schreiber AW, Parker WT, Brown AL, Butcher C, Bardy PG, Osborn M, Scott HS, Talaulikar D, Grove CS, Hahn CN, D'Andrea RJ, Ross DM. Novel modes of MPL activation in triple-negative myeloproliferative neoplasms. Pathology 2023; 55:77-85. [PMID: 36031433 DOI: 10.1016/j.pathol.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/31/2022] [Indexed: 01/11/2023]
Abstract
The identification of a somatic mutation associated with myeloid malignancy is of diagnostic importance in myeloproliferative neoplasms (MPNs). Individuals with no mutation detected in common screening tests for variants in JAK2, CALR, and MPL are described as 'triple-negative' and pose a diagnostic challenge if there is no other evidence of a clonal disorder. To identify potential drivers that might explain the clinical phenotype, we used an extended sequencing panel to characterise a cohort of 44 previously diagnosed triple-negative MPN patients for canonical mutations in JAK2, MPL and CALR at low variant allele frequency (found in 4/44 patients), less common variants in the JAK-STAT signalling pathway (12 patients), or other variants in recurrently mutated genes from myeloid malignancies (18 patients), including hotspot variants of potential clinical relevance in eight patients. In one patient with thrombocytosis we identified biallelic germline MPL variants. Neither MPL variant was activating in cell proliferation assays, and one of the variants was not expressed on the cell surface, yet co-expression of both variants led to thrombopoietin hypersensitivity. Our results highlight the clinical value of extended sequencing including germline variant analysis and illustrate the need for detailed functional assays to determine whether rare variants in JAK2 or MPL are pathogenic.
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Affiliation(s)
- Saumya E Samaraweera
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Tatjana Geukens
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Debora A Casolari
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Tran Nguyen
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Caitlyn Sun
- Department of Haematology, Royal Adelaide Hospital, Adelaide, SA, Australia; Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Sheree Bailey
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Sarah Moore
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Jinghua Feng
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA, Australia
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Wendy T Parker
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L Brown
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Carolyn Butcher
- Department of Haematology, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Peter G Bardy
- Department of Haematology, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Michael Osborn
- South Australia/Northern Territory Youth Cancer Service, Royal Adelaide Hospital, Adelaide, SA, Australia; Department of Haematology and Oncology, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Hamish S Scott
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA, Australia
| | - Dipti Talaulikar
- Haematology Translational Research Unit, ACT Pathology, Canberra Hospital, Canberra, ACT, Australia
| | - Carolyn S Grove
- Department of Haematology, Sir Charles Gairdner Hospital and PathWest, Perth, WA, Australia
| | - Christopher N Hahn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Richard J D'Andrea
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - David M Ross
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Department of Haematology, Royal Adelaide Hospital, Adelaide, SA, Australia; Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia; Department of Haematology and Genetic Pathology, Flinders University and Medical Centre, Bedford Park, SA, Australia.
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5
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Tudini E, Andrews J, Lawrence DM, King-Smith SL, Baker N, Baxter L, Beilby J, Bennetts B, Beshay V, Black M, Boughtwood TF, Brion K, Cheong PL, Christie M, Christodoulou J, Chong B, Cox K, Davis MR, Dejong L, Dinger ME, Doig KD, Douglas E, Dubowsky A, Ellul M, Fellowes A, Fisk K, Fortuno C, Friend K, Gallagher RL, Gao S, Hackett E, Hadler J, Hipwell M, Ho G, Hollway G, Hooper AJ, Kassahn KS, Krishnaraj R, Lau C, Le H, San Leong H, Lundie B, Lunke S, Marty A, McPhillips M, Nguyen LT, Nones K, Palmer K, Pearson JV, Quinn MC, Rawlings LH, Sadedin S, Sanchez L, Schreiber AW, Sigalas E, Simsek A, Soubrier J, Stark Z, Thompson BA, U J, Vakulin CG, Wells AV, Wise CA, Woods R, Ziolkowski A, Brion MJ, Scott HS, Thorne NP, Spurdle AB. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. Am J Hum Genet 2022; 109:1960-1973. [PMID: 36332611 PMCID: PMC9674965 DOI: 10.1016/j.ajhg.2022.10.006] [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] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
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Affiliation(s)
- Emma Tudini
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - James Andrews
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M. Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Sarah L. King-Smith
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Naomi Baker
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | | | - John Beilby
- PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Victoria Beshay
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Michael Black
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Tiffany F. Boughtwood
- Australian Genomics, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | | | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia,University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - John Christodoulou
- Australian Genomics, Melbourne, VIC 3052, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Kathy Cox
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Mark R. Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Lucas Dejong
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kenneth D. Doig
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Dubowsky
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Melissa Ellul
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | | | - Song Gao
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Emma Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Johanna Hadler
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael Hipwell
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Georgina Hollway
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia,Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda J. Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia,School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
| | - Karin S. Kassahn
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Rahul Krishnaraj
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Chiyan Lau
- Pathology Queensland, Brisbane, QLD 4006, Australia,The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huong Le
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Ben Lundie
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony Marty
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Mary McPhillips
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Lan T. Nguyen
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia
| | - Katia Nones
- Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristen Palmer
- Genomics Statewide Services, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - John V. Pearson
- Genome Informatics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael C.J. Quinn
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia
| | - Lesley H. Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Louisa Sanchez
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andreas W. Schreiber
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Emanouil Sigalas
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Aygul Simsek
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Julien Soubrier
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Bryony A. Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - James U
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | | | - Amanda V. Wells
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Cheryl A. Wise
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Rick Woods
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Andrew Ziolkowski
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Marie-Jo Brion
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Hamish S. Scott
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Natalie P. Thorne
- Australian Genomics, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia,Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia
| | - Amanda B. Spurdle
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia,Corresponding author
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6
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Shanmuganathan N, Wadham C, Thomson D, Shahrin NH, Vignaud C, Obourn V, Chaturvedi S, Yang F, Feng J, Saunders V, Kok CH, Yeung D, King RM, Kenyon RR, Lin M, Wang P, Scott H, Hughes T, Schreiber AW, Branford S. RNA-Based Targeted Gene Sequencing Improves the Diagnostic Yield of Mutant Detection in Chronic Myeloid Leukemia. J Mol Diagn 2022; 24:803-822. [PMID: 35550185 DOI: 10.1016/j.jmoldx.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022] Open
Abstract
Mutation detection is increasingly used for the management of hematological malignancies. Prior whole transcriptome and whole exome sequencing studies using total RNA and DNA identified diverse mutation types in cancer-related genes associated with treatment failure in patients with chronic myeloid leukemia. Variants included single-nucleotide variants and small insertions/deletions, plus fusion transcripts and partial or whole gene deletions. The hypothesis that all of these mutation types could be detected by a single cost-effective hybridization capture next-generation sequencing method using total RNA was assessed. A method was developed that targeted 130 genes relevant for myeloid and lymphoid leukemia. Retrospective samples with 121 precharacterized variants were tested using total RNA and/or DNA. Concordance of detection of precharacterized variants using RNA or DNA was 96%, whereas the enhanced sensitivity identified additional variants. Comparison between 24 matched DNA and RNA samples demonstrated 95.3% of 170 variants detectable using DNA were detected using RNA, including all but one variant predicted to activate nonsense-mediated decay. RNA identified an additional 10 variants, including fusion transcripts. Furthermore, the true effect of splice variants on RNA splicing was only evident using RNA. In conclusion, capture sequencing using total RNA alone is suitable for detecting a range of variants relevant in chronic myeloid leukemia and may be more broadly applied to other hematological malignancies where diverse variant types define risk groups.
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Daniel Thomson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Nur H Shahrin
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | | | - Vanessa Obourn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Feng Yang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jinghua Feng
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Verity Saunders
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Chung H Kok
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - David Yeung
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rob M King
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Rosalie R Kenyon
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Ming Lin
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Paul Wang
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Timothy Hughes
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Andreas W Schreiber
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
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7
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Homan CC, King-Smith SL, Lawrence DM, Arts P, Feng J, Andrews J, Armstrong M, Ha T, Dobbins J, Drazer MW, Yu K, Bödör C, Cantor A, Cazzola M, Degelman E, DiNardo CD, Duployez N, Favier R, Fröhling S, Fitzgibbon J, Klco JM, Krämer A, Kurokawa M, Lee J, Malcovati L, Morgan NV, Natsoulis G, Owen C, Patel KP, Preudhomme C, Raslova H, Rienhoff H, Ripperger T, Schulte R, Tawana K, Velloso E, Yan B, Liu P, Godley LA, Schreiber AW, Hahn CN, Scott HS, Brown AL. The RUNX1 database (RUNX1db): establishment of an expert curated RUNX1 registry and genomics database as a public resource for familial platelet disorder with myeloid malignancy. Haematologica 2021; 106:3004-3007. [PMID: 34233450 PMCID: PMC8561292 DOI: 10.3324/haematol.2021.278762] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/02/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Claire C Homan
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Sarah L King-Smith
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - David M Lawrence
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Jinghua Feng
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA
| | - James Andrews
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Mark Armstrong
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Julia Dobbins
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA
| | - Michael W Drazer
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Kai Yu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of P athology and E xperimental Cancer R esearch, Semmelweis U niversity, B udapest, H ungary
| | - Alan Cantor
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia
| | - Erin Degelman
- Division of Hematology and Hematological Malignancies, Foothills Medical Centre, Calgary, AB
| | - Courtney D DiNardo
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicolas Duployez
- Laboratory of Hematology, Biology and Pathology Center, Centre Hospitalier Regional Universitaire de Lille, Lille, France; Jean-Pierre Aubert Research Center, INSERM, Universitaire de Lille, Lille
| | - Remi Favier
- Assistance Publique- Hôpitaux de Paris, Armand Trousseau children's Hospital, Paris
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London
| | - Jeffery M Klco
- St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Dept. of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Joanne Lee
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham
| | | | - Carolyn Owen
- Division of Hematology and Hematological Malignancies, Foothills Medical Centre, Calgary, AB
| | - Keyur P Patel
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Claude Preudhomme
- Laboratory of Hematology, Biology and Pathology Center, Centre Hospitalier Regional Universitaire de Lille, Lille, France; Jean-Pierre Aubert Research Center, INSERM, Universitaire de Lille, Lille
| | - Hana Raslova
- Institut Gustave Roussy, Université Paris Sud, Equipe Labellisée par la Ligue Nationale Contre le Cancer, Villejuif
| | | | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Rachael Schulte
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, TN
| | - Kiran Tawana
- Department of Haematology, Addenbrooke's Hospital. Cambridge, CB2 0QQ
| | - Elvira Velloso
- Service of Hematology, Transfusion and Cell Therapy and Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31) HCFMUSP, University of Sao Paulo Medical School, Sao Paulo, Brazil; Genetics Laboratory, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Benedict Yan
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System
| | - Paul Liu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, Center for Clinical Cancer Genetics, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA
| | - Christopher N Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; School of Medicine, University of Adelaide, Adelaide, SA
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; School of Medicine, University of Adelaide, Adelaide, SA
| | - Anna L Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; School of Medicine, University of Adelaide, Adelaide, SA.
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8
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De Angelis C, Byrne AB, Morrow R, Feng J, Ha T, Wang P, Schreiber AW, Babic M, Taranath A, Manton N, King-Smith SL, Schwarz Q, Arts P, Scott HS, Barnett C. Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia. BMC Med Genomics 2021; 14:64. [PMID: 33639934 PMCID: PMC7916305 DOI: 10.1186/s12920-021-00911-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/25/2021] [Indexed: 12/04/2022] Open
Abstract
Background Periventricular nodular heterotopia (PNH) is a malformation of cortical development characterized by nodules of abnormally migrated neurons. The cause of posteriorly placed PNH is not well characterised and we present a case that provides insights into the cause of posterior PNH. Case presentation We report a fetus with extensive posterior PNH in association with biallelic variants in LAMC3. LAMC3 mutations have previously been shown to cause polymicrogyria and pachygyria in the occipital cortex, but not PNH. The occipital location of PNH in our case and the proposed function of LAMC3 in cortical development suggest that the identified LAMC3 variants may be causal of PNH in this fetus. Conclusion We hypothesise that this finding extends the cortical phenotype associated with LAMC3 and provides valuable insight into genetic cause of posterior PNH.
Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00911-4.
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Affiliation(s)
- Carla De Angelis
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Alicia B Byrne
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Rebecca Morrow
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Thuong Ha
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Milena Babic
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Ajay Taranath
- South Australian Medical Imaging, Women's and Children's Hospital, North Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Nick Manton
- Department of Surgical Pathology, Women's and Children's Hospital/SA Pathology, North Adelaide, SA, Australia
| | - Sarah L King-Smith
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia.,Australian Genomic Health Alliance, Melbourne, VIC, Australia
| | - Quenten Schwarz
- Neurovascular Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Peer Arts
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia.,School of Medicine, University of Adelaide, Adelaide, SA, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, VIC, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia. .,School of Medicine, University of Adelaide, Adelaide, SA, Australia. .,SA Clinical Genetics Service, Women's and Children's Hospital, 72 King William Road, North Adelaide, SA, 5006, Australia.
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9
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Thomson DW, Shahrin NH, Wang PPS, Wadham C, Shanmuganathan N, Scott HS, Dinger ME, Hughes TP, Schreiber AW, Branford S. Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia. Leukemia 2020; 34:2051-2063. [PMID: 32076119 DOI: 10.1038/s41375-020-0751-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/08/2020] [Accepted: 02/06/2020] [Indexed: 11/10/2022]
Abstract
Blast crisis of chronic myeloid leukemia is associated with poor survival and the accumulation of genomic lesions. Using whole-exome and/or RNA sequencing of patients at chronic phase (CP, n = 49), myeloid blast crisis (MBC, n = 19), and lymphoid blast crisis (LBC, n = 20), we found 25 focal gene deletions and 14 fusions in 24 patients in BC. Deletions predominated in LBC (83% of structural variants). Transcriptional analysis identified the upregulation of genes involved in V(D)J recombination, including RAG1/2 and DNTT in LBC. RAG recombination is a reported mediator of IKZF1 deletion. We investigated the extent of RAG-mediated genomic lesions in BC. Molecular hallmarks of RAG activity; DNTT-mediated nucleotide insertions and a RAG-binding motif at structural variants were exclusively found in patients with high RAG expression. Structural variants in 65% of patients in LBC displayed these hallmarks compared with only 5% in MBC. RAG-mediated events included focal deletion and novel fusion of genes associated with hematologic cancer: IKZF1, RUNX1, CDKN2A/B, and RB1. Importantly, 8/8 patients with elevated DNTT at CP diagnosis progressed to LBC by 12 months, potentially enabling early prediction of LBC. This work confirms the central mutagenic role of RAG in LBC and describes potential clinical utility in CML management.
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Affiliation(s)
- Daniel W Thomson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Nur Hezrin Shahrin
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Paul P S Wang
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Naranie Shanmuganathan
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington Campus, Sydney, NSW, Australia
| | - Timothy P Hughes
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Andreas W Schreiber
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia.
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
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10
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De Sousa SMC, Toubia J, Hardy TSE, Feng J, Wang P, Schreiber AW, Geoghegan J, Hall R, Rawlings L, Buckland M, Luxford C, Novos T, Clifton-Bligh RJ, Poplawski NK, Scott HS, Torpy DJ. Aberrant Splicing of SDHC in Families With Unexplained Succinate Dehydrogenase-Deficient Paragangliomas. J Endocr Soc 2020; 4:bvaa071. [PMID: 33195952 PMCID: PMC7646550 DOI: 10.1210/jendso/bvaa071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Context Germline mutations in the succinate dehydrogenase genes (SDHA/B/C/D, SDHAF2-collectively, "SDHx") have been implicated in paraganglioma (PGL), renal cell carcinoma (RCC), gastrointestinal stromal tumor (GIST), and pituitary adenoma (PA). Negative SDHB tumor staining is indicative of SDH-deficient tumors, usually reflecting an underlying germline SDHx mutation. However, approximately 20% of individuals with SDH-deficient tumors lack an identifiable germline SDHx mutation. Methods We performed whole-exome sequencing (WES) of germline and tumor DNA followed by Sanger sequencing validation, transcriptome analysis, metabolomic studies, and haplotype analysis in 2 Italian-Australian families with SDH-deficient PGLs and various neoplasms, including RCC, GIST, and PA. Results Germline WES revealed a novel SDHC intronic variant, which had been missed during previous routine testing, in 4 affected siblings of the index family. Transcriptome analysis demonstrated aberrant SDHC splicing, with the retained intronic segment introducing a premature stop codon. WES of available tumors in this family showed chromosome 1 deletion with loss of wild-type SDHC in a PGL and a somatic gain-of-function KIT mutation in a GIST. The SDHC intronic variant identified was subsequently detected in the second family, with haplotype analysis indicating a founder effect. Conclusions This is the deepest intronic variant to be reported among the SDHx genes. Intronic variants beyond the limits of standard gene sequencing analysis should be considered in patients with SDH-deficient tumors but negative genetic test results.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia.,Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia
| | - John Toubia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | | | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Joel Geoghegan
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Rachel Hall
- SA Pathology, Flinders Medical Centre, Bedford Park, Australia
| | | | - Michael Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, Australia.,School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Catherine Luxford
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia
| | - Talia Novos
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia
| | - Roderick J Clifton-Bligh
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia
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11
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Arts P, Garland J, Byrne AB, Hardy TS, Babic M, Feng J, Wang P, Ha T, King‐Smith SL, Schreiber AW, Crawford A, Manton N, Moore L, Barnett CP, Scott HS. Paternal mosaicism for a novel PBX1 mutation associated with recurrent perinatal death: Phenotypic expansion of the PBX1-related syndrome. Am J Med Genet A 2020; 182:1273-1277. [PMID: 32141698 PMCID: PMC7217179 DOI: 10.1002/ajmg.a.61541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/09/2020] [Accepted: 02/13/2020] [Indexed: 11/11/2022]
Abstract
Autosomal dominant (de novo) mutations in PBX1 are known to cause congenital abnormalities of the kidney and urinary tract (CAKUT), with or without extra-renal abnormalities. Using trio exome sequencing, we identified a PBX1 p.(Arg107Trp) mutation in a deceased one-day-old neonate presenting with CAKUT, asplenia, and severe bilateral diaphragmatic thinning and eventration. Further investigation by droplet digital PCR revealed that the mutation had occurred post-zygotically in the father, with different variant allele frequencies of the mosaic PBX1 mutation in blood (10%) and sperm (20%). Interestingly, the father had subclinical hydronephrosis in childhood. With an expected recurrence risk of one in five, chorionic villus sampling and prenatal diagnosis for the PBX1 mutation identified recurrence in a subsequent pregnancy. The family opted to continue the pregnancy and the second affected sibling was stillborn at 35 weeks, presenting with similar severe bilateral diaphragmatic eventration, microsplenia, and complete sex reversal (46, XY female). This study highlights the importance of follow-up studies for presumed de novo and low-level mosaic variants and broadens the phenotypic spectrum of developmental abnormalities caused by PBX1 mutations.
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Affiliation(s)
- Peer Arts
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Jessica Garland
- Paediatric and Reproductive Genetics UnitWomen's and Children's HospitalAdelaideSouth AustraliaAustralia
| | - Alicia B. Byrne
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
| | - Tristan S.E. Hardy
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- RepromedDulwichAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Milena Babic
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Jinghua Feng
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Thuong Ha
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
| | - Sarah L. King‐Smith
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
| | - Andreas W. Schreiber
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - April Crawford
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Nick Manton
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Lynette Moore
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Department of Anatomical PathologySA Pathology, Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Christopher P. Barnett
- Paediatric and Reproductive Genetics UnitWomen's and Children's HospitalAdelaideSouth AustraliaAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Hamish S. Scott
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- School of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- ACRF Cancer Genomics Facility, Centre for Cancer BiologyAn Alliance Between SA Pathology and the University of South AustraliaAdelaideSouth AustraliaAustralia
- Australian Genomics Health AllianceMelbourneVictoriaAustralia
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12
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Venugopal P, Gagliardi L, Forsyth C, Feng J, Phillips K, Babic M, Poplawski NK, Rienhoff HY, Schreiber AW, Hahn CN, Brown AL, Scott HS. Two monogenic disorders masquerading as one: severe congenital neutropenia with monocytosis and non-syndromic sensorineural hearing loss. BMC Med Genet 2020; 21:35. [PMID: 32066420 PMCID: PMC7026993 DOI: 10.1186/s12881-020-0971-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/11/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND We report a large family with four successive generations, presenting with a complex phenotype of severe congenital neutropenia (SCN), partially penetrant monocytosis, and hearing loss of varying severity. METHODS We performed whole exome sequencing to identify the causative variants. Sanger sequencing was used to perform segregation analyses on remaining family members. RESULTS We identified and classified a pathogenic GFI1 variant and a likely pathogenic variant in MYO6 which together explain the complex phenotypes seen in this family. CONCLUSIONS We present a case illustrating the benefits of a broad screening approach that allows identification of oligogenic determinants of complex human phenotypes which may have been missed if the screening was limited to a targeted gene panel with the assumption of a syndromic disorder. This is important for correct genetic diagnosis of families and disentangling the range and severity of phenotypes associated with high impact variants.
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Affiliation(s)
- Parvathy Venugopal
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Lucia Gagliardi
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia.,Endocrine and Diabetes Unit, The Queen Elizabeth Hospital, Woodville South, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
| | | | - Jinghua Feng
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, PO Box 14, Rundle Mall, Adelaide, South Australia, 5000, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, Australia
| | - Kerry Phillips
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, Australia
| | - Milena Babic
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia
| | | | | | - Andreas W Schreiber
- Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, PO Box 14, Rundle Mall, Adelaide, South Australia, 5000, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Christopher N Hahn
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,School of Medicine, University of Adelaide, Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, Australia
| | - Anna L Brown
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia. .,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, Australia. .,School of Medicine, University of Adelaide, Adelaide, Australia. .,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, PO Box 14, Rundle Mall, Adelaide, South Australia, 5000, Australia. .,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, Australia.
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13
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De Sousa SMC, Manavis J, Feng J, Wang P, Schreiber AW, Scott HS, Torpy DJ. A putative role for the aryl hydrocarbon receptor (AHR) gene in a patient with cyclical Cushing's disease. BMC Endocr Disord 2020; 20:18. [PMID: 31996203 PMCID: PMC6988286 DOI: 10.1186/s12902-020-0495-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Apart from PRKAR1A mutations in a subset of cyclical Cushing's syndrome due to primary pigmented nodular adrenocortical disease, the molecular basis of cyclical Cushing's syndrome has not been investigated. We speculated that cyclical Cushing's syndrome may be due to mutations in the clock genes that govern circadian rhythms, including the hypothalamic-pituitary-adrenal axis. CASE PRESENTATION A 47-year-old man presented with mass effects from a sellar lesion. He was ultimately diagnosed with cyclical Cushing's disease due to a giant corticotrophinoma. We performed whole exome sequencing of germline and tumour DNA, SNP array of tumour DNA and tumour immunohistochemistry in order to detect variants in candidate circadian/pituitary-associated genes. We identified a rare germline missense variant in the aryl hydrocarbon receptor (AHR) gene, which has previously been indirectly linked to pituitary tumorigenesis and clock system disruption. The AHR variant was found in a highly conserved site involved in phosphorylation. It was predicted to be damaging by multiple in silico tools and AHR tumour immunohistochemistry demonstrated loss of the normal nuclear staining pattern, suggestive of an inactivating mutation. We also found a novel, damaging germline missense variant in the retinoid X receptor gamma (RXRG) gene, multiple somatic chromosomal gains (including AHR), and a somatic mutational signature consistent with oncogenesis that may have acted synergistically with the AHR variant. CONCLUSIONS This is the first report of an AHR variant with predicted pathogenicity in the pituitary adenoma setting. Our preliminary data suggest that the highly conserved AHR gene may represent a link between pituitary tumorigenesis, the hypothalamic-pituitary-adrenal axis and the clock system. Further research may indicate a role for the gene in the development of cyclical Cushing's disease.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia.
- School of Medicine, University of Adelaide, Adelaide, Australia.
| | - Jim Manavis
- School of Medicine, University of Adelaide, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
| | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
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14
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Byrne AB, Mizumoto S, Arts P, Yap P, Feng J, Schreiber AW, Babic M, King-Smith SL, Barnett CP, Moore L, Sugahara K, Mutlu-Albayrak H, Nishimura G, Liebelt JE, Yamada S, Savarirayan R, Scott HS. Pseudodiastrophic dysplasia expands the known phenotypic spectrum of defects in proteoglycan biosynthesis. J Med Genet 2020; 57:454-460. [PMID: 31988067 PMCID: PMC7361035 DOI: 10.1136/jmedgenet-2019-106700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/09/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023]
Abstract
Background Pseudodiastrophic dysplasia (PDD) is a severe skeletal dysplasia associated with prenatal manifestation and early lethality. Clinically, PDD is classified as a ‘dysplasia with multiple joint dislocations’; however, the molecular aetiology of the disorder is currently unknown. Methods Whole exome sequencing (WES) was performed on three patients from two unrelated families, clinically diagnosed with PDD, in order to identify the underlying genetic cause. The functional effects of the identified variants were characterised using primary cells and human cell-based overexpression assays. Results WES resulted in the identification of biallelic variants in the established skeletal dysplasia genes, B3GAT3 (family 1) and CANT1 (family 2). Mutations in these genes have previously been reported to cause ‘multiple joint dislocations, short stature, and craniofacial dysmorphism with or without congenital heart defects’ (‘JDSCD’; B3GAT3) and Desbuquois dysplasia 1 (CANT1), disorders in the same nosological group as PDD. Follow-up of the B3GAT3 variants demonstrated significantly reduced B3GAT3/GlcAT-I expression. Downstream in vitro functional analysis revealed abolished biosynthesis of glycosaminoglycan side chains on proteoglycans. Functional evaluation of the CANT1 variant showed impaired nucleotidase activity, which results in inhibition of glycosaminoglycan synthesis through accumulation of uridine diphosphate. Conclusion For the families described in this study, the PDD phenotype was caused by mutations in the known skeletal dysplasia genes B3GAT3 and CANT1, demonstrating the advantage of genomic analyses in delineating the molecular diagnosis of skeletal dysplasias. This finding expands the phenotypic spectrum of B3GAT3-related and CANT1-related skeletal dysplasias to include PDD and highlights the significant phenotypic overlap of conditions within the proteoglycan biosynthesis pathway.
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Affiliation(s)
- Alicia B Byrne
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan.,Research Center for Pathogenesis of Intractable Diseases, Meijo University, Nagoya, Japan.,Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Patrick Yap
- Victorian Clinical Genetics Service, Royal Children's Hospital, Melbourne, Victoria, Australia.,Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jinghua Feng
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Andreas W Schreiber
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Sarah L King-Smith
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia.,School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lynette Moore
- School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia.,Department of Surgical Pathology, Women's and Children's Hospital, SA Pathology, North Adelaide, South Australia, Australia
| | - Kazuyuki Sugahara
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Hatice Mutlu-Albayrak
- Department of Pediatric Genetics, Cengiz Gökcek Obstetrics and Children's Hospital, Gaziantep, Turkey
| | - Gen Nishimura
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Jan E Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan.,Research Center for Pathogenesis of Intractable Diseases, Meijo University, Nagoya, Japan
| | - Ravi Savarirayan
- Victorian Clinical Genetics Service, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia .,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia.,School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
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15
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De Sousa SMC, Wang PPS, Santoreneos S, Shen A, Yates CJ, Babic M, Eshraghi L, Feng J, Koszyca B, Roberts-Thomson S, Schreiber AW, Torpy DJ, Scott HS. The Genomic Landscape of Sporadic Prolactinomas. Endocr Pathol 2019; 30:318-328. [PMID: 31473917 DOI: 10.1007/s12022-019-09587-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Somatic GNAS and USP8 mutations have been implicated in sporadic somatotrophinomas and corticotrophinomas, respectively. However, no genes are known to be recurrently mutated in sporadic prolactinomas. The prevalence of copy number variants (CNV), which is emerging as a mechanism of tumorigenesis in sporadic pituitary adenomas in general, is also unclear in prolactinomas. To characterize the genetic events underpinning sporadic prolactinomas, we performed whole exome sequencing of paired tumor and germline DNA from 12 prolactinoma patients. We observed recurrent large-scale CNV, most commonly in the form of copy number gains. We also identified sequence variants of interest in 15 genes. This included the DRD2, PRL, TMEM67, and MLH3 genes with plausible links to prolactinoma formation. Of the 15 genes of interest, CNV was seen at the gene locus in the corresponding tumor in 10 cases, and pituitary expression of eight genes was in the top 10% of tissues. However, none of our shortlisted somatic variants appeared to be classical driver mutations as no variant was found in more than one tumor. Future directions of research include mechanistic studies to investigate how CNV may contribute to prolactinoma formation, larger studies of relevant prolactinoma subsets according to clinical characteristics, and additional genetic investigations for aberrations not captured by whole exome sequencing.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia.
- School of Medicine, University of Adelaide, Adelaide, Australia.
| | - Paul P S Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | | | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | - Leila Eshraghi
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Barbara Koszyca
- Department of Anatomical Pathology, Royal Adelaide Hospital, Adelaide, Australia
| | | | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
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16
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Cheah JJC, Brown AL, Schreiber AW, Feng J, Babic M, Moore S, Young CC, Fine M, Phillips K, Guandalini M, Wilson P, Poplawski N, Hahn CN, Scott HS. A novel germline SAMD9L mutation in a family with ataxia-pancytopenia syndrome and pediatric acute lymphoblastic leukemia. Haematologica 2019; 104:e318-e321. [PMID: 30923096 DOI: 10.3324/haematol.2018.207316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jesse J C Cheah
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA.,Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, SA
| | - Anna L Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA.,Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, SA.,School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA
| | - Andreas W Schreiber
- School of Biological Sciences, University of Adelaide, Adelaide, SA.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA
| | - Milena Babic
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA
| | - Sarah Moore
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA
| | - Chun-Chun Young
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA
| | - Miriam Fine
- Adult Genetics Unit, Royal Adelaide Hospital, University of Adelaide, Adelaide, SA
| | - Kerry Phillips
- Adult Genetics Unit, Royal Adelaide Hospital, University of Adelaide, Adelaide, SA
| | - Michael Guandalini
- Children's Health Queensland Hospital and Health Service, Lady Cilento Children's Hospital Brisbane, Brisbane, QLD
| | - Peter Wilson
- Children's Cancer Services, Lady Cilento Children's Hospital Brisbane, Brisbane, QLD
| | - Nicola Poplawski
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA.,Adult Genetics Unit, Royal Adelaide Hospital, University of Adelaide, Adelaide, SA
| | - Christopher N Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA.,Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, SA.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA .,Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, SA.,School of Biological Sciences, University of Adelaide, Adelaide, SA.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA.,School of Medicine, University of Adelaide, Adelaide, SA, Australia
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17
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Pillman KA, Phillips CA, Roslan S, Toubia J, Dredge BK, Bert AG, Lumb R, Neumann DP, Li X, Conn SJ, Liu D, Bracken CP, Lawrence DM, Stylianou N, Schreiber AW, Tilley WD, Hollier BG, Khew-Goodall Y, Selth LA, Goodall GJ, Gregory PA. miR-200/375 control epithelial plasticity-associated alternative splicing by repressing the RNA-binding protein Quaking. EMBO J 2018; 37:embj.201899016. [PMID: 29871889 PMCID: PMC6028027 DOI: 10.15252/embj.201899016] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 12/25/2022] Open
Abstract
Members of the miR‐200 family are critical gatekeepers of the epithelial state, restraining expression of pro‐mesenchymal genes that drive epithelial–mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR‐200c and another epithelial‐enriched miRNA, miR‐375, exert widespread control of alternative splicing in cancer cells by suppressing the RNA‐binding protein Quaking (QKI). During EMT, QKI‐5 directly binds to and regulates hundreds of alternative splicing targets and exerts pleiotropic effects, such as increasing cell migration and invasion and restraining tumour growth, without appreciably affecting mRNA levels. QKI‐5 is both necessary and sufficient to direct EMT‐associated alternative splicing changes, and this splicing signature is broadly conserved across many epithelial‐derived cancer types. Importantly, several actin cytoskeleton‐associated genes are directly targeted by both QKI and miR‐200c, revealing coordinated control of alternative splicing and mRNA abundance during EMT. These findings demonstrate the existence of a miR‐200/miR‐375/QKI axis that impacts cancer‐associated epithelial cell plasticity through widespread control of alternative splicing.
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Affiliation(s)
- Katherine A Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Caroline A Phillips
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Suraya Roslan
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Daniel P Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Xiaochun Li
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Simon J Conn
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Dawei Liu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.,Discipline of Medicine, The University of Adelaide, Adelaide, SA, Australia
| | - David M Lawrence
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Nataly Stylianou
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Qld, Australia
| | - Andreas W Schreiber
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.,Freemasons Foundation Centre for Men's Health, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Brett G Hollier
- Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Qld, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.,Discipline of Medicine, The University of Adelaide, Adelaide, SA, Australia.,School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.,Freemasons Foundation Centre for Men's Health, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia .,Discipline of Medicine, The University of Adelaide, Adelaide, SA, Australia.,School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia .,Discipline of Medicine, The University of Adelaide, Adelaide, SA, Australia
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18
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De Sousa SMC, Stowasser M, Feng J, Schreiber AW, Wang P, Hahn CN, Gordon RD, Torpy DJ, Scott HS, Gagliardi L. ARMC5 is not implicated in familial hyperaldosteronism type II (FH-II). J Hum Hypertens 2017; 31:857-859. [DOI: 10.1038/jhh.2017.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Venugopal P, Moore S, Lawrence DM, George AJ, Hannan RD, Bray SC, To LB, D'Andrea RJ, Feng J, Tirimacco A, Yeoman AL, Young CC, Fine M, Schreiber AW, Hahn CN, Barnett C, Saxon B, Scott HS. Self-reverting mutations partially correct the blood phenotype in a Diamond Blackfan anemia patient. Haematologica 2017; 102:e506-e509. [PMID: 28971907 DOI: 10.3324/haematol.2017.166678] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Parvathy Venugopal
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Sarah Moore
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - David M Lawrence
- School of Biological Sciences, University of Adelaide, SA 5005, Australia.,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Amee J George
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia.,Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.,School of Biomedical Sciences, University of Queensland, St. Lucia, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia.,Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.,School of Biomedical Sciences, University of Queensland, St. Lucia, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Sarah Ce Bray
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Medicine, University of Adelaide, Australia
| | - Luen Bik To
- School of Medicine, University of Adelaide, Australia.,Division of Haematology, SA Pathology, Adelaide, Australia
| | - Richard J D'Andrea
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,Division of Haematology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia
| | - Jinghua Feng
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia
| | - Amanda Tirimacco
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Alexandra L Yeoman
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Chun Chun Young
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Miriam Fine
- South Australian Clinical Genetics Service, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Andreas W Schreiber
- School of Biological Sciences, University of Adelaide, SA 5005, Australia.,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia
| | - Christopher N Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Medicine, University of Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia
| | - Christopher Barnett
- School of Medicine, University of Adelaide, Australia.,South Australian Clinical Genetics Service, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Ben Saxon
- School of Medicine, University of Adelaide, Australia.,Department of Haematology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia .,Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, SA 5005, Australia.,School of Medicine, University of Adelaide, Australia.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia
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20
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Oftedal BE, Ardesjö Lundgren B, Hamm D, Gan PY, Holdsworth SR, Hahn CN, Schreiber AW, Scott HS. T cell receptor assessment in autoimmune disease requires access to the most adjacent immunologically active organ. J Autoimmun 2017; 81:24-33. [DOI: 10.1016/j.jaut.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 01/22/2023]
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21
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Scott HS, Brown AL, Hiwase D, Schreiber AW, Feng J, Babic M, Moore S, Geoghegan J, Parker W, Branford S, Hahn CN. The challenges of identifying mosaicism in haematological malignancies. Pathology 2017. [DOI: 10.1016/j.pathol.2016.12.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Scott HS, Brown AL, Hiwase D, Schreiber AW, Feng J, Babic M, Poplawski N, Fine M, Rawlings L, Branford S, Fuller S, Lewis I, D’Andrea RJ, Hahn CN. Familial clustering of haematological malignancies: harbingers of wider germline cancer susceptibility. Pathology 2017. [DOI: 10.1016/j.pathol.2016.12.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Barnett CP, Nataren NJ, Klingler-Hoffmann M, Schwarz Q, Chong CE, Lee YK, Bruno DL, Lipsett J, McPhee AJ, Schreiber AW, Feng J, Hahn CN, Scott HS. Cover Image, Volume 37, Issue 9. Hum Mutat 2016. [DOI: 10.1002/humu.23058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Barnett CP, Nataren NJ, Klingler-Hoffmann M, Schwarz Q, Chong CE, Lee YK, Bruno DL, Lipsett J, McPhee AJ, Schreiber AW, Feng J, Hahn CN, Scott HS. Ectrodactyly and Lethal Pulmonary Acinar Dysplasia Associated with Homozygous FGFR2 Mutations Identified by Exome Sequencing. Hum Mutat 2016; 37:955-63. [PMID: 27323706 DOI: 10.1002/humu.23032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 02/11/2016] [Revised: 05/31/2016] [Accepted: 06/04/2016] [Indexed: 12/26/2022]
Abstract
Ectrodactyly/split hand-foot malformation is genetically heterogeneous with more than 100 syndromic associations. Acinar dysplasia is a rare congenital lung lesion of unknown etiology, which is frequently lethal postnatally. To date, there have been no reports of combinations of these two phenotypes. Here, we present an infant from a consanguineous union with both ectrodactyly and autopsy confirmed acinar dysplasia. SNP array and whole-exome sequencing analyses of the affected infant identified a novel homozygous Fibroblast Growth Factor Receptor 2 (FGFR2) missense mutation (p.R255Q) in the IgIII domain (D3). Expression studies of Fgfr2 in development show localization to the affected limbs and organs. Molecular modeling and genetic and functional assays support that this mutation is at least a partial loss-of-function mutation, and contributes to ectrodactyly and acinar dysplasia only in homozygosity, unlike previously reported heterozygous activating FGFR2 mutations that cause Crouzon, Apert, and Pfeiffer syndromes. This is the first report of mutations in a human disease with ectrodactyly with pulmonary acinar dysplasia and, as such, homozygous loss-of-function FGFR2 mutations represent a unique syndrome.
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Affiliation(s)
- Christopher P Barnett
- SA Clinical Genetics, Women's and Children's Hospital/SA Pathology, North Adelaide, SA, Australia.,School of Biological Sciences, University of Adelaide, SA, Australia
| | - Nathalie J Nataren
- School of Biological Sciences, University of Adelaide, SA, Australia.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia
| | - Manuela Klingler-Hoffmann
- School of Biological Sciences, University of Adelaide, SA, Australia.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia
| | - Quenten Schwarz
- Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia
| | - Chan-Eng Chong
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - Young K Lee
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - Damien L Bruno
- Cytogenetics Laboratory, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Jill Lipsett
- Department of Neonatal Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Andrew J McPhee
- School of Medicine, University of Adelaide, SA, Australia.,Department of Anatomical Pathology, Women's and Children's Hospital/SA Pathology, North Adelaide, SA, Australia
| | - Andreas W Schreiber
- School of Biological Sciences, University of Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, SA, Australia
| | - Jinghua Feng
- School of Biological Sciences, University of Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, SA, Australia
| | - Christopher N Hahn
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia.,School of Medicine, University of Adelaide, SA, Australia
| | - Hamish S Scott
- School of Biological Sciences, University of Adelaide, SA, Australia.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia.,Centre for Cancer Biology, An Alliance between SA Pathology and the University of South Australia, SA, Australia.,School of Medicine, University of Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, SA, Australia
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25
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Wang PPS, Parker WT, Branford S, Schreiber AW. BAM-matcher: a tool for rapid NGS sample matching. Bioinformatics 2016; 32:2699-701. [PMID: 27153667 DOI: 10.1093/bioinformatics/btw239] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/25/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED The standard method used by high-throughput genome sequencing facilities for detecting mislabelled samples is to use independently generated high-density SNP data to determine sample identity. However, as it has now become commonplace to have multiple samples sequenced from the same source, such as for analysis of somatic variants using matched tumour and normal samples, we can directly use the genotype information inherent in the sequence data to match samples and thus bypass the need for additional laboratory testing. Here we present BAM-matcher, a tool that can rapidly determine whether two BAM files represent samples from the same biological source by comparing their genotypes. BAM-matcher is designed to be simple to use, provides easily interpretable results, and is suitable for deployment at early stages of data processing pipelines. AVAILABILITY AND IMPLEMENTATION BAM-matcher is licensed under the Creative Commons by Attribution license, and is available from: https://bitbucket.org/sacgf/bam-matcher SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT paul.wang@sa.gov.au.
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Affiliation(s)
- Paul P S Wang
- Department of Genetics and Molecular Pathology, and ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Wendy T Parker
- Department of Genetics and Molecular Pathology, and ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia, School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology, and School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia, School of Biological Sciences and School of Medicine, University of Adelaide, Adelaide, Australia
| | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia, School of Biological Sciences and
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26
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Plett D, Baumann U, Schreiber AW, Holtham L, Kalashyan E, Toubia J, Nau J, Beatty M, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN. Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. Plant Biotechnol J 2016; 14:342-53. [PMID: 26038196 DOI: 10.1111/pbi.12388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 05/10/2023]
Abstract
Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression.
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Affiliation(s)
- Darren Plett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Luke Holtham
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Elena Kalashyan
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Toubia
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Nau
- DuPont Pioneer, Johnston, IA, USA
| | | | | | | | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Trevor Garnett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Brent N Kaiser
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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27
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Ricos MG, Hodgson BL, Pippucci T, Saidin A, Ong YS, Heron SE, Licchetta L, Bisulli F, Bayly MA, Hughes J, Baldassari S, Palombo F, Santucci M, Meletti S, Berkovic SF, Rubboli G, Thomas PQ, Scheffer IE, Tinuper P, Geoghegan J, Schreiber AW, Dibbens LM. Mutations in the mammalian target of rapamycin pathway regulators NPRL2 and NPRL3 cause focal epilepsy. Ann Neurol 2015; 79:120-31. [PMID: 26505888 DOI: 10.1002/ana.24547] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/29/2015] [Accepted: 10/17/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Focal epilepsies are the most common form observed and have not generally been considered to be genetic in origin. Recently, we identified mutations in DEPDC5 as a cause of familial focal epilepsy. In this study, we investigated whether mutations in the mammalian target of rapamycin (mTOR) regulators, NPRL2 and NPRL3, also contribute to cases of focal epilepsy. METHODS We used targeted capture and next-generation sequencing to analyze 404 unrelated probands with focal epilepsy. We performed exome sequencing on two families with multiple members affected with focal epilepsy and linkage analysis on one of these. RESULTS In our cohort of 404 unrelated focal epilepsy patients, we identified five mutations in NPRL2 and five in NPRL3. Exome sequencing analysis of two families with focal epilepsy identified NPRL2 and NPRL3 as the top candidate-causative genes. Some patients had focal epilepsy associated with brain malformations. We also identified 18 new mutations in DEPDC5. INTERPRETATION We have identified NPRL2 and NPRL3 as two new focal epilepsy genes that also play a role in the mTOR-signaling pathway. Our findings show that mutations in GATOR1 complex genes are the most significant cause of familial focal epilepsy identified to date, including cases with brain malformations. It is possible that deregulation of cellular growth control plays a more important role in epilepsy than is currently recognized.
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Affiliation(s)
- Michael G Ricos
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - Bree L Hodgson
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi University Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Akzam Saidin
- Novocraft Technologies Sdn Bhd, Selangor, Malaysia
| | - Yeh Sze Ong
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - Sarah E Heron
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - Laura Licchetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bisulli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marta A Bayly
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - James Hughes
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Sara Baldassari
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi University Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Flavia Palombo
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi University Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | - Margherita Santucci
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Stefano Meletti
- Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, AUSL Modena, Modena, Italy
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Guido Rubboli
- Danish Epilepsy Center, Filadelfia/University of Copenhagen, Dianalund, Denmark.,IRCCS Institute of Neurological Sciences, Neurology Unit, Bellaria Hospital, Bologna, Italy
| | - Paul Q Thomas
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Paolo Tinuper
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Joel Geoghegan
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Andreas W Schreiber
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Leanne M Dibbens
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, Australia.,Molecular Neurogenomics Research Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
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28
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Ross DM, Altamura HK, Hahn CN, Nicola M, Yeoman AL, Holloway MR, Geoghegan J, Feng J, Schreiber AW, Branford S, Moore S, Scott HS. Delayed diagnosis leading to accelerated-phase chronic eosinophilic leukemia due to a cytogenetically cryptic, imatinib-responsive TNIP1-PDFGRB fusion gene. Leukemia 2015; 30:1402-5. [PMID: 26503642 DOI: 10.1038/leu.2015.301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- D M Ross
- Haematology Directorate, SA Pathology, Adelaide, South Australia, Australia.,Flinders University and Medical Centre, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - H K Altamura
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - C N Hahn
- School of Medicine, University of Adelaide, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia.,Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - M Nicola
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - A L Yeoman
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - M R Holloway
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - J Geoghegan
- Australian Cancer Research Foundation Genomics Facility, SA Pathology, Adelaide, South Australia, Australia
| | - J Feng
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,Australian Cancer Research Foundation Genomics Facility, SA Pathology, Adelaide, South Australia, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - A W Schreiber
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,Australian Cancer Research Foundation Genomics Facility, SA Pathology, Adelaide, South Australia, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - S Branford
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia.,Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, South Australia, Australia
| | - S Moore
- Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - H S Scott
- School of Medicine, University of Adelaide, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia.,Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.,Australian Cancer Research Foundation Genomics Facility, SA Pathology, Adelaide, South Australia, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, South Australia, Australia
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29
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Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ. The RNA binding protein quaking regulates formation of circRNAs. Cell 2015; 160:1125-34. [PMID: 25768908 DOI: 10.1016/j.cell.2015.02.014] [Citation(s) in RCA: 1436] [Impact Index Per Article: 159.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/05/2015] [Accepted: 02/03/2015] [Indexed: 12/19/2022]
Abstract
Circular RNAs (circRNAs), formed by non-sequential back-splicing of pre-mRNA transcripts, are a widespread form of non-coding RNA in animal cells. However, it is unclear whether the majority of circRNAs represent splicing by-products without function or are produced in a regulated manner to carry out specific cellular functions. We show that hundreds of circRNAs are regulated during human epithelial-mesenchymal transition (EMT) and find that the production of over one-third of abundant circRNAs is dynamically regulated by the alternative splicing factor, Quaking (QKI), which itself is regulated during EMT. Furthermore, by modulating QKI levels, we show the effect on circRNA abundance is dependent on intronic QKI binding motifs. Critically, the addition of QKI motifs is sufficient to induce de novo circRNA formation from transcripts that are normally linearly spliced. These findings demonstrate circRNAs are both purposefully synthesized and regulated by cell-type specific mechanisms, suggesting they play specific biological roles in EMT.
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Affiliation(s)
- Simon J Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia
| | - Vanessa M Conn
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Marika Salmanidis
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Caroline A Phillips
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Suraya Roslan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; Department of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia; Department of Medicine, University of Adelaide, Adelaide, SA 5005, Australia.
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30
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Gagliardi L, Nataren N, Feng J, Schreiber AW, Hahn CN, Conwell LS, Coman D, Scott HS. Allan-Herndon-Dudley syndrome with unusual profound sensorineural hearing loss. Am J Med Genet A 2015; 167A:1872-6. [DOI: 10.1002/ajmg.a.37075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 03/07/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Lucia Gagliardi
- Endocrine and Metabolic Unit; Royal Adelaide Hospital; North Terrace Adelaide Australia
- Department of Genetics and Molecular Pathology; Centre for Cancer Biology; SA Pathology; Adelaide Australia
- School of Medicine; University of Adelaide; Adelaide Australia
| | - Nathalie Nataren
- Department of Genetics and Molecular Pathology; Centre for Cancer Biology; SA Pathology; Adelaide Australia
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide Australia
| | - Jinghua Feng
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide Australia
- South Australian Cancer Genomics Facility; Centre for Cancer Biology, SA Pathology; Adelaide Australia
| | - Andreas W. Schreiber
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide Australia
- South Australian Cancer Genomics Facility; Centre for Cancer Biology, SA Pathology; Adelaide Australia
| | - Christopher N. Hahn
- Department of Genetics and Molecular Pathology; Centre for Cancer Biology; SA Pathology; Adelaide Australia
- School of Medicine; University of Adelaide; Adelaide Australia
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide Australia
| | - Louise S. Conwell
- Department of Endocrinology and Diabetes and Queensland Children's Medical Research Institute; Royal Children's Hospital; Brisbane Australia
- School of Medicine; University of Queensland; Brisbane Australia
| | - David Coman
- School of Medicine; University of Queensland; Brisbane Australia
- Department of Metabolic Medicine; Royal Children's Hospital; Brisbane Australia
- School of Medicine; Griffith University; Gold Coast Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology; Centre for Cancer Biology; SA Pathology; Adelaide Australia
- School of Medicine; University of Adelaide; Adelaide Australia
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide Australia
- South Australian Cancer Genomics Facility; Centre for Cancer Biology, SA Pathology; Adelaide Australia
- School of Pharmacy and Medical Sciences; Division of Health Sciences; University of South Australia; Adelaide Australia
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31
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Gagliardi L, Schreiber AW, Hahn CN, Feng J, Cranston T, Boon H, Hotu C, Oftedal BE, Cutfield R, Adelson DL, Braund WJ, Gordon RD, Rees DA, Grossman AB, Torpy DJ, Scott HS. ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J Clin Endocrinol Metab 2014; 99:E1784-92. [PMID: 24905064 DOI: 10.1210/jc.2014-1265] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT Bilateral macronodular adrenal hyperplasia (BMAH) is a rare form of adrenal Cushing's syndrome. Familial cases have been reported, but at the time we conducted this study, the genetic basis of BMAH was unknown. Recently, germline variants of armadillo repeat containing 5 (ARMC5) in patients with isolated BMAH and somatic, second-hit mutations in tumor nodules, were identified. OBJECTIVE Our objective was to identify the genetic basis of familial BMAH. DESIGN We performed whole exome capture and sequencing of 2 affected individuals from each of 4 BMAH families (BMAH-01, BMAH-02, BMAH-03, and BMAH-05). Based on clinical evaluation, there were 7, 3, 3, and 4 affected individuals in these families, respectively. Sanger sequencing of ARMC5 was performed in 1 other BMAH kindred, BMAH-06. RESULTS Exome sequencing identified novel variants Chr16:g.31477540, c.2139delT, p.(Thr715Leufs*1) (BMAH-02) and Chr16:g.31473811, c.943C→T, p.(Arg315Trp) (BMAH-03) in ARMC5 (GRch37/hg19), validated by Sanger sequencing. BMAH-01 had a recently reported mutation Chr16:g.31476121, c.1777C→T, p.(Arg593Trp). Sanger sequencing of ARMC5 in BMAH-06 identified a previously reported mutation, Chr16:g. 31473688; c.799C→T, p.(Arg267*). The genetic basis of BMAH in BMAH-05 was not identified. CONCLUSIONS Our studies have detected ARMC5 mutations in 4 of 5 BMAH families tested, confirming that these mutations are a frequent cause of BMAH. Two of the 4 families had novel mutations, indicating allelic heterogeneity. Preclinical evaluation did not predict mutation status. The ARMC5-negative family had unusual prominent hyperaldosteronism. Further studies are needed to determine the penetrance of BMAH in ARMC5 mutation-positive relatives of affected patients, the practical utility of genetic screening and genotype-phenotype correlations.
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Affiliation(s)
- Lucia Gagliardi
- Endocrine and Metabolic Unit (L.G., D.J.T.), Royal Adelaide Hospital; Department of Genetics and Molecular Pathology (L.G., C.N.H., B.E.O., H.S.S.) and ACRF Cancer Genomics Facility (A.W.S., J.F., H.S.S.), Centre for Cancer Biology, SA Pathology; and School of Pharmacy and Medical Sciences (H.S.S.), Division of Health Sciences, University of South Australia, Adelaide SA 5000, Australia; Schools of Medicine (L.G., C.N.H., D.J.T., H.S.S.) and Molecular and Biomedical Science (A.W.S., J.F., D.L.A., H.S.S.), University of Adelaide SA 5005, Australia; Oxford Medical Genetics Laboratories (T.C., H.B.), Oxford University Hospitals National Health Service Trust, and Oxford Centre for Diabetes, Endocrinology and Metabolism (A.B.G.), Churchill Hospital, University of Oxford, Oxford OX3 7LE, United Kingdom; Department of Endocrinology (C.H.), Greenlane Clinical Centre, Auckland District Health Board, Auckland 1051, New Zealand; Department of Clinical Science (B.E.O.), University of Bergen, 5021 Bergen, Norway; Department of Endocrinology (R.C.), North Shore Hospital, Waitemata District Health Board, Auckland 0622, New Zealand; Department of Endocrinology (W.J.B.), Flinders Medical Centre, Bedford Park, SA 5042 Australia; School of Medicine (R.D.G.), University of Queensland, Brisbane QLD 4072, Australia; Endocrine Hypertension Research Centre (R.D.G.), Greenslopes and Princess Alexandra Hospitals, Brisbane QLD 4120, Australia; and Centre for Endocrine and Diabetes Sciences (D.A.R.), School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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Abstract
BACKGROUND Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors from true biological variants is a challenging task. For organisms without a reference genome this difficulty is even more challenging. RESULTS We have developed a method for the correction of sequencing errors in data from the Illumina Solexa sequencing platforms. It does not require a reference genome and is of relevance for microRNA studies, unsequenced genomes, variant detection in ultra-deep sequencing and even for RNA-Seq studies of organisms with sequenced genomes where RNA editing is being considered. CONCLUSIONS The derived error model is novel in that it allows different error probabilities for each position along the read, in conjunction with different error rates depending on the particular nucleotides involved in the substitution, and does not force these effects to behave in a multiplicative manner. The model provides error rates which capture the complex effects and interactions of the three main known causes of sequencing error associated with the Illumina platforms.
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Affiliation(s)
- Julie A Sleep
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Urrbrae, SA 5064, Australia
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Andreas W Schreiber
- ACRF South Australian Cancer Genome Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5000, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Urrbrae, SA 5064, Australia
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33
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Pishas KI, Neuhaus SJ, Clayer MT, Schreiber AW, Lawrence DM, Perugini M, Whitfield RJ, Farshid G, Manavis J, Chryssidis S, Mayo BJ, Haycox RC, Ho K, Brown MP, D'Andrea RJ, Evdokiou A, Thomas DM, Desai J, Callen DF, Neilsen PM. Nutlin-3a efficacy in sarcoma predicted by transcriptomic and epigenetic profiling. Cancer Res 2013; 74:921-31. [PMID: 24336067 DOI: 10.1158/0008-5472.can-13-2424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nutlin-3a is a small-molecule antagonist of p53/MDM2 that is being explored as a treatment for sarcoma. In this study, we examined the molecular mechanisms underlying the sensitivity of sarcomas to Nutlin-3a. In an ex vivo tissue explant system, we found that TP53 pathway alterations (TP53 status, MDM2/MDM4 genomic amplification/mRNA overexpression, MDM2 SNP309, and TP53 SNP72) did not confer apoptotic or cytostatic responses in sarcoma tissue biopsies (n = 24). Unexpectedly, MDM2 status did not predict Nutlin-3a sensitivity. RNA sequencing revealed that the global transcriptomic profiles of these sarcomas provided a more robust prediction of apoptotic responses to Nutlin-3a. Expression profiling revealed a subset of TP53 target genes that were transactivated specifically in sarcomas that were highly sensitive to Nutlin-3a. Of these target genes, the GADD45A promoter region was shown to be hypermethylated in 82% of wild-type TP53 sarcomas that did not respond to Nutlin-3a, thereby providing mechanistic insight into the innate ability of sarcomas to resist apoptotic death following Nutlin-3a treatment. Collectively, our findings argue that the existing benchmark biomarker for MDM2 antagonist efficacy (MDM2 amplification) should not be used to predict outcome but rather global gene expression profiles and epigenetic status of sarcomas dictate their sensitivity to p53/MDM2 antagonists.
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Affiliation(s)
- Kathleen I Pishas
- Authors' Affiliations: Sarcoma Research Group, Discipline of Medicine, Centre for Personalised Cancer Medicine, Faculty of Health Sciences, School of Molecular and Biomedical Science, Departments of Orthopaedics and Trauma and Haematology, Cancer Clinical Trials Unit, Royal Adelaide Hospital; Department of Surgery, Royal Adelaide Hospital and University of Adelaide; ACRF Cancer Genomics Facility, Centre for Cancer Biology, Division of Tissue Pathology, SA Pathology; Centre for Neurological Diseases, Hanson Institute and SA Pathology; Department of Radiology, Queen Elizabeth Hospital; Department of Haematology and Oncology, Basil Hetzel Institute and Queen Elizabeth Hospital; University of Adelaide, Discipline of Surgery, Basil Hetzel Institute, Adelaide; Sarcoma Genomics and Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia; and Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, Australia
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Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL. A comparative analysis of algorithms for somatic SNV detection in cancer. ACTA ACUST UNITED AC 2013; 29:2223-30. [PMID: 23842810 PMCID: PMC3753564 DOI: 10.1093/bioinformatics/btt375] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [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] [Indexed: 02/04/2023]
Abstract
Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates. Availability: Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/ Contact:david.adelson@adelaide.edu.au Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicola D Roberts
- School of Molecular and Biomedical Science and School of Mathematical Sciences, University of Adelaide, South Australia, Australia
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Huynh BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis JCR, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. Plant Mol Biol 2012; 80:299-314. [PMID: 22864927 DOI: 10.1007/s11103-012-9949-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/23/2012] [Indexed: 05/21/2023]
Abstract
Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors' knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
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Affiliation(s)
- Bao-Lam Huynh
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond 5064, South Australia,
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Schreiber AW, Hayden MJ, Forrest KL, Kong SL, Langridge P, Baumann U. Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. BMC Genomics 2012; 13:492. [PMID: 22989011 PMCID: PMC3505470 DOI: 10.1186/1471-2164-13-492] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 04/10/2012] [Accepted: 09/14/2012] [Indexed: 01/08/2023] Open
Abstract
Background Bread wheat is one of the world’s most important food crops and considerable efforts have been made to develop genomic resources for this species. This includes an on-going project by the International Wheat Genome Sequencing Consortium to assemble its large and complex genome, which is hexaploid and contains three closely related ‘homoeologous’ copies for each chromosome. This multi-national effort avoids the complications polyploidy entails for correct assembly of the genome by sequencing flow-sorted chromosome arms one at a time. Here we report on an alternate approach, a direct homoeolog-specific assembly of the expressed portion of the genome, the transcriptome. Results After assessment of the ability of various assemblers to generate homoeolog-specific assemblies, we employed a two-stage assembly process to produce a high-quality assembly of the transcriptome of hexaploid wheat from Roche-454 and Illumina GAIIx paired-end sequence reads. The assembly process made use of a rapid partitioning of expressed sequences into homoeologous clusters, followed by a parallel high-fidelity assembly of each cluster on a 1150-processor compute cloud. We assessed assembly quality through comparison to known wheat gene sequences and found that in ca. 98.5% of cases the assembly was sufficiently accurate for homoeologous triplets to be cleanly separated into either two or three separate contigs. Comparison to publicly available transcript collections suggests that the assembly covers ~75-80% of the complete transcriptome. Conclusions This work therefore describes the first homoeolog-specific sequence assembly of the wheat transcriptome and provides a reference transcriptome for future wheat research. Furthermore, our assembly methodology is transferable to other polyploid organisms.
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Affiliation(s)
- Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Univ. of Adelaide, PMB 1 Glen Osmond, SA 5064, Australia.
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Conn SJ, Gilliham M, Athman A, Schreiber AW, Baumann U, Moller I, Cheng NH, Stancombe MA, Hirschi KD, Webb AAR, Burton R, Kaiser BN, Tyerman SD, Leigh RA. Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis. Plant Cell 2011; 23:240-57. [PMID: 21258004 PMCID: PMC3051233 DOI: 10.1105/tpc.109.072769] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 11/15/2010] [Accepted: 12/17/2010] [Indexed: 05/18/2023]
Abstract
The physiological role and mechanism of nutrient storage within vacuoles of specific cell types is poorly understood. Transcript profiles from Arabidopsis thaliana leaf cells differing in calcium concentration ([Ca], epidermis <10 mM versus mesophyll >60 mM) were compared using a microarray screen and single-cell quantitative PCR. Three tonoplast-localized Ca(2+) transporters, CAX1 (Ca(2+)/H(+)-antiporter), ACA4, and ACA11 (Ca(2+)-ATPases), were identified as preferentially expressed in Ca-rich mesophyll. Analysis of respective loss-of-function mutants demonstrated that only a mutant that lacked expression of both CAX1 and CAX3, a gene ectopically expressed in leaves upon knockout of CAX1, had reduced mesophyll [Ca]. Reduced capacity for mesophyll Ca accumulation resulted in reduced cell wall extensibility, stomatal aperture, transpiration, CO(2) assimilation, and leaf growth rate; increased transcript abundance of other Ca(2+) transporter genes; altered expression of cell wall-modifying proteins, including members of the pectinmethylesterase, expansin, cellulose synthase, and polygalacturonase families; and higher pectin concentrations and thicker cell walls. We demonstrate that these phenotypes result from altered apoplastic free [Ca(2+)], which is threefold greater in cax1/cax3 than in wild-type plants. We establish CAX1 as a key regulator of apoplastic [Ca(2+)] through compartmentation into mesophyll vacuoles, a mechanism essential for optimal plant function and productivity.
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Affiliation(s)
- Simon J Conn
- School of Agriculture, Food, and Wine, University of Adelaide, Glen Osmond, South Australia 5064, Australia
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Schreiber AW, Sutton T, Caldo RA, Kalashyan E, Lovell B, Mayo G, Muehlbauer GJ, Druka A, Waugh R, Wise RP, Langridge P, Baumann U. Comparative transcriptomics in the Triticeae. BMC Genomics 2009; 10:285. [PMID: 19558723 PMCID: PMC2717122 DOI: 10.1186/1471-2164-10-285] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [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: 02/18/2009] [Accepted: 06/29/2009] [Indexed: 01/13/2023] Open
Abstract
Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring). For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex) using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able to distinguish contributions from individual homoeologs. Furthermore, the comparison between the two species leads us to conclude that the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels, presumably reflecting increased selection pressure on genes coding for proteins present at high levels. In addition, the results indicate the presence of a correlation between sequence and expression conservation within the Triticeae.
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Affiliation(s)
- Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Univ of Adelaide, PMB 1 Glen Osmond, SA 5064, Australia.
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Abstract
MOTIVATION Global gene expression measurements as obtained, for example, in microarray experiments can provide important clues to the underlying transcriptional control mechanisms and network structure of a biological cell. In the absence of a detailed understanding of this gene regulation, current attempts at classification of expression data rely on clustering and pattern recognition techniques employing ad-hoc similarity criteria. To improve this situation, a better understanding of the expected relationships between expression profiles of genes associated by biological function is required. RESULTS It is shown that perturbation expansions familiar from biological systems theory make precise predictions for the types of relationships to be expected for expression profiles of biologically associated genes, even if the underlying biological factors responsible for this association are not known. Classification criteria are derived, most of which are not usually employed in clustering algorithms. The approach is illustrated by using the AtGenExpress Arabidopsis thaliana developmental expression map.
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Affiliation(s)
- Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Hartley Grove, PMB 1 Waite Campus, The University of Adelaide Glen Osmond 5064, Australia.
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Weyrauch M, Schreiber AW. Comment on "unique translation between Hamiltonian operators and functional integrals". Phys Rev Lett 2002; 88:078901. [PMID: 11863945 DOI: 10.1103/physrevlett.88.078901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2001] [Indexed: 05/23/2023]
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Rosenfelder R, Schreiber AW. Polaron variational methods in the particle representation of field theory. I. General formalism. Phys Rev D Part Fields 1996; 53:3337-3353. [PMID: 10020328 DOI: 10.1103/physrevd.53.3337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Rosenfelder R, Schreiber AW. Polaron variational methods in the particle representation of field theory. II. Numerical results for the propagator. Int J Clin Exp Med 1996; 53:3354-3365. [PMID: 10020329 DOI: 10.1103/physrevd.53.3354] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Schreiber AW, Mulders PJ, Signal AI, Thomas AW. Pion cloud of the nucleon and its effect on deep-inelastic structure. Phys Rev D Part Fields 1992; 45:3069-3078. [PMID: 10014708 DOI: 10.1103/physrevd.45.3069] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Schreiber AW, Thomas AW, Londergan JT. QCD evolution of the spin structure functions of the neutron and proton. Phys Rev D Part Fields 1990; 42:2226-2236. [PMID: 10013076 DOI: 10.1103/physrevd.42.2226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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