1
|
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.
| |
Collapse
|
2
|
Bagdonaite I, Marinova IN, Rudjord-Levann AM, Pallesen EMH, King-Smith SL, Karlsson R, Rømer TB, Chen YH, Miller RL, Olofsson S, Nordén R, Bergström T, Dabelsteen S, Wandall HH. Glycoengineered keratinocyte library reveals essential functions of specific glycans for all stages of HSV-1 infection. Nat Commun 2023; 14:7000. [PMID: 37919266 PMCID: PMC10622544 DOI: 10.1038/s41467-023-42669-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
Viral and host glycans represent an understudied aspect of host-pathogen interactions, despite potential implications for treatment of viral infections. This is due to lack of easily accessible tools for analyzing glycan function in a meaningful context. Here we generate a glycoengineered keratinocyte library delineating human glycosylation pathways to uncover roles of specific glycans at different stages of herpes simplex virus type 1 (HSV-1) infectious cycle. We show the importance of cellular glycosaminoglycans and glycosphingolipids for HSV-1 attachment, N-glycans for entry and spread, and O-glycans for propagation. While altered virion surface structures have minimal effects on the early interactions with wild type cells, mutation of specific O-glycosylation sites affects glycoprotein surface expression and function. In conclusion, the data demonstrates the importance of specific glycans in a clinically relevant human model of HSV-1 infection and highlights the utility of genetic engineering to elucidate the roles of specific viral and cellular carbohydrate structures.
Collapse
Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Irina N Marinova
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Asha M Rudjord-Levann
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Emil M H Pallesen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Sarah L King-Smith
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Troels B Rømer
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Sigvard Olofsson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-41346, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-41346, Gothenburg, Sweden
| | - Tomas Bergström
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-41346, Gothenburg, Sweden
| | - Sally Dabelsteen
- Department of Odontology, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
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.
| |
Collapse
|
6
|
Homan CC, Venugopal P, Arts P, Shahrin NH, Feurstein S, Rawlings L, Lawrence DM, Andrews J, King-Smith SL, Harvey NL, Brown AL, Scott HS, Hahn CN. GATA2 deficiency syndrome: A decade of discovery. Hum Mutat 2021; 42:1399-1421. [PMID: 34387894 PMCID: PMC9291163 DOI: 10.1002/humu.24271] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 02/24/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/14/2022]
Abstract
GATA2 deficiency syndrome (G2DS) is a rare autosomal dominant genetic disease predisposing to a range of symptoms, of which myeloid malignancy and immunodeficiency including recurrent infections are most common. In the last decade since it was first reported, there have been over 480 individuals identified carrying a pathogenic or likely pathogenic germline GATA2 variant with symptoms of G2DS, with 240 of these confirmed to be familial and 24 de novo. For those that develop myeloid malignancy (75% of all carriers with G2DS disease symptoms), the median age of onset is 17 years (range 0-78 years) and myelodysplastic syndrome is the first diagnosis in 75% of these cases with acute myeloid leukemia in a further 9%. All variant types appear to predispose to myeloid malignancy and immunodeficiency. Apart from lymphedema in which haploinsufficiency seems necessary, the mutational requirements of the other less common G2DS phenotypes is still unclear. These predominantly loss-of-function variants impact GATA2 expression and function in numerous ways including perturbations to DNA binding, protein structure, protein:protein interactions, and gene transcription, splicing, and expression. In this review, we provide the first expert-curated ACMG/AMP classification with codes of published variants compatible for use in clinical or diagnostic settings.
Collapse
Affiliation(s)
- Claire C Homan
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Parvathy Venugopal
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Nur H Shahrin
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Simone Feurstein
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Lesley Rawlings
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia
| | - David M Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia
| | - James Andrews
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia
| | - Sarah L King-Smith
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia.,Specialist Genomics, Australian Genomics, 50 Flemington Road, Parkville, Victoria, 3052, Australia
| | - Natasha L Harvey
- Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Anna L Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, University of Adelaide, Adelaide, South Australia, 5000, Australia.,Clinical Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia.,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Specialist Genomics, Australian Genomics, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Adelaide Medical School, University of Adelaide, Adelaide, South Australia, 5000, Australia.,Clinical Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Christopher N Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia.,Molecular Pathology Research Laboratory, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, University of Adelaide, Adelaide, South Australia, 5000, Australia.,Clinical Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|