1
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Dias KR, Shrestha R, Schofield D, Evans CA, O'Heir E, Zhu Y, Zhang F, Standen K, Weisburd B, Stenton SL, Sanchis-Juan A, Brand H, Talkowski ME, Ma A, Ghedia S, Wilson M, Sandaradura SA, Smith J, Kamien B, Turner A, Bakshi M, Adès LC, Mowat D, Regan M, McGillivray G, Savarirayan R, White SM, Tan TY, Stark Z, Brown NJ, Pérez-Jurado LA, Krzesinski E, Hunter MF, Akesson L, Fennell AP, Yeung A, Boughtwood T, Ewans LJ, Kerkhof J, Lucas C, Carey L, French H, Rapadas M, Stevanovski I, Deveson IW, Cliffe C, Elakis G, Kirk EP, Dudding-Byth T, Fletcher J, Walsh R, Corbett MA, Kroes T, Gecz J, Meldrum C, Cliffe S, Wall M, Lunke S, North K, Amor DJ, Field M, Sadikovic B, Buckley MF, O'Donnell-Luria A, Roscioli T. Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort. Genet Med 2024; 26:101076. [PMID: 38258669 DOI: 10.1016/j.gim.2024.101076] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
PURPOSE Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively. METHODS ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID. RESULTS The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis. CONCLUSION Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.
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Affiliation(s)
- Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Rupendra Shrestha
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ying Zhu
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Futao Zhang
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Krystle Standen
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Sondy Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia; Northern Clinical School, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia
| | - Sarah A Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - Janine Smith
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, WA, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | - Lesley C Adès
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Melbourne, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, SA, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Lauren Akesson
- Melbourne Pathology, Melbourne, VIC, Australia; Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia; Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Paul Fennell
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiffany Boughtwood
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Lisa J Ewans
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia; Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada
| | - Christopher Lucas
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Louise Carey
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Hugh French
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Corrina Cliffe
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - George Elakis
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Edwin P Kirk
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Janice Fletcher
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rebecca Walsh
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Thessa Kroes
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Cliff Meldrum
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Simon Cliffe
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Meg Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Kathryn North
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia; Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Michael Field
- The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia.
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2
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El‐Wahsh S, Fellner A, Hobbs M, Copty J, Deveson I, Stevanovski I, Stoll M, Zhu D, Narayanan RK, Grosz B, Worgan L, Cheong PL, Yeow D, Rudaks L, Hasan MM, Hayes VM, Kennerson M, Kumar KR, Hayes M. An Inversion Affecting the GCH1 Gene as a Novel Finding in Dopa-Responsive Dystonia. Mov Disord Clin Pract 2024; 11:582-585. [PMID: 38497520 PMCID: PMC11078477 DOI: 10.1002/mdc3.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Shadi El‐Wahsh
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Avi Fellner
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- The Neurogenetics Clinic, Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson HospitalPetah TikvaIsrael
| | - Matthew Hobbs
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Joe Copty
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Ira Deveson
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Igor Stevanovski
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Marion Stoll
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Danqing Zhu
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Ramesh K. Narayanan
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Bianca Grosz
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Lisa Worgan
- Clinical Genetics ServiceRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
- Department of Medical GenomicsRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
| | - Pak Leng Cheong
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Royal Prince Alfred Hospital, New South Wales Health PathologySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Dennis Yeow
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Neuroscience Research AustraliaSydneyNew South WalesAustralia
| | - Laura Rudaks
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
| | - Md Mehedi Hasan
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Vanessa M. Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
- School of Health Systems & Public HealthUniversity of PretoriaPretoriaSouth Africa
- Manchester Cancer Research CentreUniversity of ManchesterManchesterUK
| | - Marina Kennerson
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Kishore R. Kumar
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Michael Hayes
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
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3
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Gunter HM, Youlten SE, Reis ALM, McCubbin T, Madala BS, Wong T, Stevanovski I, Cipponi A, Deveson IW, Santini NS, Kummerfeld S, Croucher PI, Marcellin E, Mercer TR. A universal molecular control for DNA, mRNA and protein expression. Nat Commun 2024; 15:2480. [PMID: 38509097 PMCID: PMC10954659 DOI: 10.1038/s41467-024-46456-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
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Affiliation(s)
- Helen M Gunter
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott E Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Ted Wong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Arcadi Cipponi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Nadia S Santini
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAP, Ciudad de México, 04010, Mexico
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Esteban Marcellin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tim R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia.
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia.
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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4
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Reis ALM, Rapadas M, Hammond JM, Gamaarachchi H, Stevanovski I, Ayuputeri Kumaheri M, Chintalaphani SR, Dissanayake DSB, Siggs OM, Hewitt AW, Llamas B, Brown A, Baynam G, Mann GJ, McMorran BJ, Easteal S, Hermes A, Jenkins MR, Patel HR, Deveson IW. The landscape of genomic structural variation in Indigenous Australians. Nature 2023; 624:602-610. [PMID: 38093003 PMCID: PMC10733147 DOI: 10.1038/s41586-023-06842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
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Affiliation(s)
- Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Hasindu Gamaarachchi
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Meutia Ayuputeri Kumaheri
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Sanjog R Chintalaphani
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Duminda S B Dissanayake
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Owen M Siggs
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Bastien Llamas
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Alex Brown
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Gareth Baynam
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Genetic Services of Western Australia, Western Australian Department of Health, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Western Australia, Australia
| | - Graham J Mann
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Brendan J McMorran
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Misty R Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
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5
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Dominik N, Magri S, Currò R, Abati E, Facchini S, Corbetta M, Macpherson H, Di Bella D, Sarto E, Stevanovski I, Chintalaphani SR, Akcimen F, Manini A, Vegezzi E, Quartesan I, Montgomery KA, Pirota V, Crespan E, Perini C, Grupelli GP, Tomaselli PJ, Marques W, Shaw J, Polke J, Salsano E, Fenu S, Pareyson D, Pisciotta C, Tofaris GK, Nemeth AH, Ealing J, Radunovic A, Kearney S, Kumar KR, Vucic S, Kennerson M, Reilly MM, Houlden H, Deveson I, Tucci A, Taroni F, Cortese A. Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis. Brain 2023; 146:5060-5069. [PMID: 37450567 PMCID: PMC10689911 DOI: 10.1093/brain/awad240] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 03/27/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing data from nearly 10 000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n = 6 from five families), AAGGC (n = 2 from one family) and AGAGG (n = 1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, we revealed a pathogenic role for large AAAGG repeat configuration expansions (n = 5). Long-read sequencing was used to characterize the entire repeat sequence, and six patients exhibited a pure AGGGC expansion, while the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs appeared to have arisen from a common haplotype and were predicted to form highly stable G quadruplexes, which have previously been demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions when the AAAGG motif is very large (>500 repeats) or the AAGGG motif is interrupted. Accurate sizing and full sequencing of the satellite repeat with long-read sequencing is recommended in clinically selected cases to enable accurate molecular diagnosis and counsel patients and their families.
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Affiliation(s)
- Natalia Dominik
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Riccardo Currò
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
| | - Stefano Facchini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- IRCCS Mondino Foundation, Pavia 27100,
Italy
| | - Marinella Corbetta
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Hannah Macpherson
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Elisa Sarto
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Sanjog R Chintalaphani
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Fulya Akcimen
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, MD 2292, USA
| | - Arianna Manini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto
Auxologico Italiano, Milan 20145, Italy
| | | | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Kylie-Ann Montgomery
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Valentina Pirota
- Department of Chemistry, University of Pavia,
Pavia 27100, Italy
- G4-INTERACT, USERN, 27100 Pavia,
Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Glenda Paola Grupelli
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Pedro J Tomaselli
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Joseph Shaw
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - James Polke
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ettore Salsano
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Silvia Fenu
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Davide Pareyson
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Chiara Pisciotta
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - George K Tofaris
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS
Foundation Trust, Oxford OX3 7HE, UK
| | - John Ealing
- Salford Royal NHS Foundation Trust Greater Manchester Neuroscience Centre,
Manchester Centre for Clinical Neurosciences Salford, Greater
Manchester M6 8HD, UK
| | | | - Seamus Kearney
- Department of Neurology, Royal Victoria Hospital,
Belfast BT12 6BA, UK
| | - Kishore R Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical
Research, Darlinghurst, NSW 2010, Australia
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
| | - Steve Vucic
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
- Brain and Nerve Research Centre, Concord Hospital,
Sydney, NSW 2139, Australia
| | - Marina Kennerson
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute
SLHD, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2050, Australia
| | - Mary M Reilly
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ira Deveson
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
| | - Arianna Tucci
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Andrea Cortese
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
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6
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Scriba CK, Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ghaoui R, Ghia D, Henderson RD, Jordan N, Winkel A, Lamont PJ, Rodrigues MJ, Roxburgh RH, Weisburd B, Laing NG, Deveson IW, Davis MR, Ravenscroft G. RFC1 in an Australasian neurological disease cohort: extending the genetic heterogeneity and implications for diagnostics. Brain Commun 2023; 5:fcad208. [PMID: 37621409 PMCID: PMC10445415 DOI: 10.1093/braincomms/fcad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome is a progressive, generally late-onset, neurological disorder associated with biallelic pentanucleotide expansions in Intron 2 of the RFC1 gene. The locus exhibits substantial genetic variability, with multiple pathogenic and benign pentanucleotide repeat alleles previously identified. To determine the contribution of pathogenic RFC1 expansions to neurological disease within an Australasian cohort and further investigate the heterogeneity exhibited at the locus, a combination of flanking and repeat-primed PCR was used to screen a cohort of 242 Australasian patients with neurological disease. Patients whose data indicated large gaps within expanded alleles following repeat-primed PCR, underwent targeted long-read sequencing to identify novel repeat motifs at the locus. To increase diagnostic yield, additional probes at the RFC1 repeat region were incorporated into the PathWest diagnostic laboratory targeted neurological disease gene panel to enable first-pass screening of the locus for all samples tested on the panel. Within the Australasian cohort, we detected known pathogenic biallelic expansions in 15.3% (n = 37) of patients. Thirty indicated biallelic AAGGG expansions, two had biallelic 'Māori alleles' [(AAAGG)exp(AAGGG)exp], two samples were compound heterozygous for the Māori allele and an AAGGG expansion, two samples had biallelic ACAGG expansions and one sample was compound heterozygous for the ACAGG and AAGGG expansions. Forty-five samples tested indicated the presence of biallelic expansions not known to be pathogenic. A large proportion (84%) showed complex interrupted patterns following repeat-primed PCR, suggesting that these expansions are likely to be comprised of more than one repeat motif, including previously unknown repeats. Using targeted long-read sequencing, we identified three novel repeat motifs in expanded alleles. Here, we also show that short-read sequencing can be used to reliably screen for the presence or absence of biallelic RFC1 expansions in all samples tested using the PathWest targeted neurological disease gene panel. Our results show that RFC1 pathogenic expansions make a substantial contribution to neurological disease in the Australasian population and further extend the heterogeneity of the locus. To accommodate the increased complexity, we outline a multi-step workflow utilizing both targeted short- and long-read sequencing to achieve a definitive genotype and provide accurate diagnoses for patients.
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Affiliation(s)
- Carolin K Scriba
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Sanjog R Chintalaphani
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Roula Ghaoui
- Department of Neurology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Darshan Ghia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
- Neurology and Stroke Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Robert D Henderson
- Centre for Clinical Research, University of Queensland, Herston, QLD 4006, Australia
| | - Nerissa Jordan
- Department of Neurology, Fiona Stanley Hospital, Perth, WA 6150, Australia
| | - Antony Winkel
- Department of Neurosciences, Griffith University, Sunshine Coast University Hospital, Mount Gravatt, QLD 4111, Australia
| | | | | | - Richard H Roxburgh
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nigel G Laing
- Preventive Genetics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Mark R Davis
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Gianina Ravenscroft
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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7
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Hort Y, Sullivan P, Wedd L, Fowles L, Stevanovski I, Deveson I, Simons C, Mallett A, Patel C, Furlong T, Cowley MJ, Shine J, Mallawaarachchi A. Atypical splicing variants in PKD1 explain most undiagnosed typical familial ADPKD. NPJ Genom Med 2023; 8:16. [PMID: 37419908 DOI: 10.1038/s41525-023-00362-z] [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: 12/20/2022] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic cause of kidney failure and is primarily associated with PKD1 or PKD2. Approximately 10% of patients remain undiagnosed after standard genetic testing. We aimed to utilise short and long-read genome sequencing and RNA studies to investigate undiagnosed families. Patients with typical ADPKD phenotype and undiagnosed after genetic diagnostics were recruited. Probands underwent short-read genome sequencing, PKD1 and PKD2 coding and non-coding analyses and then genome-wide analysis. Targeted RNA studies investigated variants suspected to impact splicing. Those undiagnosed then underwent Oxford Nanopore Technologies long-read genome sequencing. From over 172 probands, 9 met inclusion criteria and consented. A genetic diagnosis was made in 8 of 9 (89%) families undiagnosed on prior genetic testing. Six had variants impacting splicing, five in non-coding regions of PKD1. Short-read genome sequencing identified novel branchpoint, AG-exclusion zone and missense variants generating cryptic splice sites and a deletion causing critical intron shortening. Long-read sequencing confirmed the diagnosis in one family. Most undiagnosed families with typical ADPKD have splice-impacting variants in PKD1. We describe a pragmatic method for diagnostic laboratories to assess PKD1 and PKD2 non-coding regions and validate suspected splicing variants through targeted RNA studies.
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Affiliation(s)
- Yvonne Hort
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Laura Wedd
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Igor Stevanovski
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Ira Deveson
- Genomic Technologies, Garvan Institute of Medical Research, Sydney, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Andrew Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Timothy Furlong
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - John Shine
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia
| | - Amali Mallawaarachchi
- Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, Australia.
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, Australia.
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8
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Folland C, Ganesh V, Weisburd B, McLean C, Kornberg AJ, O'Donnell-Luria A, Rehm HL, Stevanovski I, Chintalaphani SR, Kennedy P, Deveson IW, Ravenscroft G. Transcriptome and Genome Analysis Uncovers a DMD Structural Variant: A Case Report. Neurol Genet 2023; 9:e200064. [PMID: 37090938 PMCID: PMC10117699 DOI: 10.1212/nxg.0000000000200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 03/16/2023]
Abstract
Objective Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the dystrophin gene (DMD). Hypermethylated CGG expansions within DIP2B 5' UTR are associated with an intellectual development disorder. Here, we demonstrate the diagnostic utility of genomic short-read sequencing (SRS) and transcriptome sequencing to identify a novel DMD structural variant (SV) and a DIP2B CGG expansion in a patient with DMD for whom conventional diagnostic testing failed to yield a genetic diagnosis. Methods We performed genomic SRS, skeletal muscle transcriptome sequencing, and targeted programmable long-read sequencing (LRS). Results The proband had a typical DMD clinical presentation, autism spectrum disorder (ASD), and dystrophinopathy on muscle biopsy. Transcriptome analysis identified 6 aberrantly expressed genes; DMD and DIP2B were the strongest underexpression and overexpression outliers, respectively. Genomic SRS identified a 216 kb paracentric inversion (NC_000023.11: g.33162217-33378800) overlapping 2 DMD promoters. ExpansionHunter indicated an expansion of 109 CGG repeats within the 5' UTR of DIP2B. Targeted genomic LRS confirmed the SV and genotyped the DIP2B repeat expansion as 270 CGG repeats. Discussion Here, transcriptome data heavily guided genomic analysis to resolve a complex DMD inversion and a DIP2B repeat expansion. Longitudinal follow-up will be important for clarifying the clinical significance of the DIP2B genotype.
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Affiliation(s)
- Chiara Folland
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Vijay Ganesh
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ben Weisburd
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Catriona McLean
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Andrew J Kornberg
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Anne O'Donnell-Luria
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Heidi L Rehm
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Igor Stevanovski
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Sanjog R Chintalaphani
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Paul Kennedy
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ira W Deveson
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
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9
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Williams LJ, Qiu J, Ong TL, Deveson IW, Stevanovski I, Chintalaphani SR, Fellner A, Varikatt W, Morales‐Briceno H, Tchan M, Kumar KR, Fung VS. NOTCH2NLC GGC Repeat Expansion Presenting as Adult-Onset Cervical Dystonia. Mov Disord Clin Pract 2023; 10:704-706. [PMID: 37070059 PMCID: PMC10105096 DOI: 10.1002/mdc3.13677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Affiliation(s)
- Laura J. Williams
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Jessica Qiu
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Tien Lee Ong
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Ira W. Deveson
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
- St. Vincent's Clinical School, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Igor Stevanovski
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - Sanju R. Chintalaphani
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
- St. Vincent's Clinical School, Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Avi Fellner
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
- Raphael Recanati Genetics Institute, Rabin Medical CenterBeilinson HospitalPetah TikvaIsrael
- The Neurology Department, Rabin Medical CenterBeilinson HospitalPetah TikvaIsrael
| | - Winny Varikatt
- Tissue Pathology and Diagnostic Oncology, Institute of Clinical Pathology and Medical ResearchWestmead HospitalWestmeadNew South WalesAustralia
- Sydney Medical SchoolThe University of SydneySydneyNew South WalesAustralia
| | - Hugo Morales‐Briceno
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Michel Tchan
- Sydney Medical SchoolThe University of SydneySydneyNew South WalesAustralia
- Department of Medical GeneticsWestmead HospitalWestmeadNew South WalesAustralia
| | - Kishore R. Kumar
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
- Sydney Medical SchoolThe University of SydneySydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord HospitalConcordNew South WalesAustralia
- Neurology Department, Central Clinical School, Concord Repatriation General HospitalUniversity of SydneyConcordNew South WalesAustralia
| | - Victor S.C. Fung
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
- Sydney Medical SchoolThe University of SydneySydneyNew South WalesAustralia
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10
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Reis AL, Hammond JH, Stevanovski I, Arnold JC, McGregor IS, Deveson IW, Gururajan A. Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition. iScience 2022; 25:104861. [PMID: 36039298 PMCID: PMC9418440 DOI: 10.1016/j.isci.2022.104861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/03/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Our understanding of the molecular pathology of posttraumatic stress disorder (PTSD) is evolving due to advances in sequencing technologies. With the recent emergence of Oxford Nanopore direct RNA-seq (dRNA-seq), it is now also possible to interrogate diverse RNA modifications, collectively known as the “epitranscriptome.”. Here, we present our analyses of the male and female mouse amygdala transcriptome and epitranscriptome, obtained using parallel Illumina RNA-seq and Oxford Nanopore dRNA-seq, associated with the acquisition of PTSD-like fear induced by Pavlovian cued-fear conditioning. We report significant sex-specific differences in the amygdala transcriptional response during fear acquisition and a range of shared and dimorphic epitranscriptomic signatures. Differential RNA modifications are enriched among mRNA transcripts associated with neurotransmitter regulation and mitochondrial function, many of which have been previously implicated in PTSD. Very few differentially modified transcripts are also differentially expressed, suggesting an influential, expression-independent role for epitranscriptional regulation in PTSD-like fear acquisition. PTSD-like trauma has sexually dimorphic effects on the amygdala transcriptome Most RNA modifications identified adhere to the known patterns associated with m6A There was enrichment of RNA modifications in neurological/PTSD-related genes There was little overlap between transcriptomic and epitranscriptomic signatures
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11
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Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ferguson JM, Pineda SS, Scriba CK, Tchan M, Fung V, Ng K, Cortese A, Houlden H, Dobson-Stone C, Fitzpatrick L, Halliday G, Ravenscroft G, Davis MR, Laing NG, Fellner A, Kennerson M, Kumar KR, Deveson IW. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci Adv 2022; 8:eabm5386. [PMID: 35245110 PMCID: PMC8896783 DOI: 10.1126/sciadv.abm5386] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care.
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Affiliation(s)
- Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sanjog R. Chintalaphani
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M. Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Carolin K. Scriba
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Michel Tchan
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Victor Fung
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital and The University of Sydney, Sydney, NSW, Australia
| | - Andrea Cortese
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Lauren Fitzpatrick
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Glenda Halliday
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Mark R. Davis
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Nigel G. Laing
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Avi Fellner
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- The Neurology Department, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Faculty of Health and Medicine, University of Sydney, Camperdown, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
- Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW, Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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12
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Grosz BR, Stevanovski I, Negri S, Ellis M, Barnes S, Reddel S, Vucic S, Nicholson GA, Cortese A, Kumar KR, Deveson IW, Kennerson ML. Long read sequencing overcomes challenges in the diagnosis of
SORD
neuropathy. J Peripher Nerv Syst 2022; 27:120-126. [DOI: 10.1111/jns.12485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/13/2022] [Accepted: 02/22/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Bianca R Grosz
- Northcott Neuroscience Laboratory ANZAC Research Institute Concord NSW Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research Sydney NSW Australia
| | - Sara Negri
- Istituiti Clinici Scientifici Maugeri IRCCS Environmental Research Center Pavia Italy
| | - Melina Ellis
- Northcott Neuroscience Laboratory ANZAC Research Institute Concord NSW Australia
- Sydney Medical School University of Sydney Camperdown NSW Australia
| | - Stephanie Barnes
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Department of Neurology Concord Repatriation General Hospital Concord NSW Australia
- Faculty of Medicine University of Notre Dame Sydney Australia
- Department of Neurology Hornsby Ku‐ring‐Gai Hospital Sydney Australia
| | - Stephen Reddel
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Department of Neurology Concord Repatriation General Hospital Concord NSW Australia
| | - Steve Vucic
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Department of Neurology Concord Repatriation General Hospital Concord NSW Australia
| | - Garth A Nicholson
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Department of Neurology Concord Repatriation General Hospital Concord NSW Australia
- Molecular Medicine Laboratory Concord Repatriation General Hospital Concord NSW Australia
| | - Andrea Cortese
- MRC Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology London UK
- Department of Brain and Behavioral Sciences University of Pavia Pavia Italy
| | - Kishore R Kumar
- Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research Sydney NSW Australia
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Department of Neurology Concord Repatriation General Hospital Concord NSW Australia
- Molecular Medicine Laboratory Concord Repatriation General Hospital Concord NSW Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research Sydney NSW Australia
- St Vincent’s Clinical School University of New South Wales Sydney NSW Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory ANZAC Research Institute Concord NSW Australia
- Sydney Medical School University of Sydney Camperdown NSW Australia
- Molecular Medicine Laboratory Concord Repatriation General Hospital Concord NSW Australia
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13
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Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ, Mercer TR, Xu J. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol 2021; 39:1115-1128. [PMID: 33846644 PMCID: PMC8434938 DOI: 10.1038/s41587-021-00857-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
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Affiliation(s)
- Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, China
| | | | - James C Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA
| | | | | | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - James Blackburn
- Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Michael Hubank
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | | | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, China
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lihyun Sun
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Hanane Arib
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hunter Best
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA
| | - Fergal Casey
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jonathan Choi
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | - Jorge Dinis
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Feng
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | | | | | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Garima Kushwaha
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiguang Li
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Charles Ma
- Cancer Genetics, Inc., Rutherford, NJ, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA
| | | | | | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paula Z Proszek
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), University of Helsinki, Helsinki, Finland
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Tieliu Shi
- Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Melissa Smith
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Maya Strahl
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Jiashi Wang
- Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chang Xu
- Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
| | | | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
| | - Yilin Zhang
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Timothy R Mercer
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
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14
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Bull RA, Adikari TN, Ferguson JM, Hammond JM, Stevanovski I, Beukers AG, Naing Z, Yeang M, Verich A, Gamaarachchi H, Kim KW, Luciani F, Stelzer-Braid S, Eden JS, Rawlinson WD, van Hal SJ, Deveson IW. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat Commun 2020; 11:6272. [PMID: 33298935 PMCID: PMC7726558 DOI: 10.1038/s41467-020-20075-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/11/2020] [Indexed: 01/15/2023] Open
Abstract
Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. We report that, despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.
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Affiliation(s)
- Rowena A Bull
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Thiruni N Adikari
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - James M Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jillian M Hammond
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Alicia G Beukers
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Zin Naing
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Malinna Yeang
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Andrey Verich
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Ki Wook Kim
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sacha Stelzer-Braid
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity & Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Centre for Virus Research, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - William D Rawlinson
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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15
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Yee C, Main NM, Terry A, Stevanovski I, Maczurek A, Morgan AJ, Calabro S, Potter AJ, Iemma TL, Bowen DG, Ahlenstiel G, Warner FJ, McCaughan GW, McLennan SV, Shackel NA. CD147 mediates intrahepatic leukocyte aggregation and determines the extent of liver injury. PLoS One 2019; 14:e0215557. [PMID: 31291257 PMCID: PMC6619953 DOI: 10.1371/journal.pone.0215557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/24/2019] [Indexed: 01/26/2023] Open
Abstract
Background Chronic inflammation is the driver of liver injury and results in progressive fibrosis and eventual cirrhosis with consequences including both liver failure and liver cancer. We have previously described increased expression of the highly multifunctional glycoprotein CD147 in liver injury. This work describes a novel role of CD147 in liver inflammation and the importance of leukocyte aggregates in determining the extent of liver injury. Methods Non-diseased, progressive injury, and cirrhotic liver from humans and mice were examined using a mAb targeting CD147. Inflammatory cell subsets were assessed by multiparameter flow cytometry. Results In liver injury, we observe abundant, intrahepatic leukocyte clusters defined as ≥5 adjacent CD45+ cells which we have termed “leukocyte aggregates”. We have shown that these leukocyte aggregates have a significant effect in determining the extent of liver injury. If CD147 is blocked in vivo, these leukocyte aggregates diminish in size and number, together with a marked significant reduction in liver injury including fibrosis. This is accompanied by no change in overall intrahepatic leukocyte numbers. Further, blocking of aggregation formation occurs prior to an appreciable increase in inflammatory markers or fibrosis. Additionally, there were no observed, “off-target” or unpredicted effects in targeting CD147. Conclusion CD147 mediates leukocyte aggregation which is associated with the development of liver injury. This is not a secondary effect, but a cause of injury as aggregate formation proceeds other markers of injury. Leukocyte aggregation has been previously described in inflammation dating back over many decades. Here we demonstrate that leukocyte aggregates determine the extent of liver injury.
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Affiliation(s)
- Christine Yee
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
- Gastroenterology and Liver Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Nathan M. Main
- Gastroenterology and Liver Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Alexandra Terry
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
- Gastroenterology and Liver Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Igor Stevanovski
- Gastroenterology and Liver Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Annette Maczurek
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - Alison J. Morgan
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - Sarah Calabro
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - Alison J. Potter
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - Tina L. Iemma
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - David G. Bowen
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
- A.W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Golo Ahlenstiel
- Western Sydney School of Medicine, Blacktown Hospital, Blacktown, NSW, Australia
| | - Fiona J. Warner
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
| | - Geoffrey W. McCaughan
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
- A.W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Susan V. McLennan
- Department of Endocrinology, Department of Medicine and Bosch Institute, Royal Prince Alfred Hospital, The University of Sydney, NSW, Australia
| | - Nicholas A. Shackel
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, NSW, Australia
- Gastroenterology and Liver Laboratory, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- A.W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Liverpool Hospital, Liverpool, NSW, Australia
- * E-mail:
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16
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Thientosapol ES, Sharbeen G, Lau KKE, Bosnjak D, Durack T, Stevanovski I, Weninger W, Jolly CJ. Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2. Nucleic Acids Res 2017; 45:3146-3157. [PMID: 28039326 PMCID: PMC5389528 DOI: 10.1093/nar/gkw1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022] Open
Abstract
AID deaminates C to U in either strand of Ig genes, exclusively producing C:G/G:C to T:A/A:T transition mutations if U is left unrepaired. Error-prone processing by UNG2 or mismatch repair diversifies mutation, predominantly at C:G or A:T base pairs, respectively. Here, we show that transversions at C:G base pairs occur by two distinct processing pathways that are dictated by sequence context. Within and near AGCT mutation hotspots, transversion mutation at C:G was driven by UNG2 without requirement for mismatch repair. Deaminations in AGCT were refractive both to processing by UNG2 and to high-fidelity base excision repair (BER) downstream of UNG2, regardless of mismatch repair activity. We propose that AGCT sequences resist faithful BER because they bind BER-inhibitory protein(s) and/or because hemi-deaminated AGCT motifs innately form a BER-resistant DNA structure. Distal to AGCT sequences, transversions at G were largely co-dependent on UNG2 and mismatch repair. We propose that AGCT-distal transversions are produced when apyrimidinic sites are exposed in mismatch excision patches, because completion of mismatch repair would require bypass of these sites.
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Affiliation(s)
- Eddy Sanchai Thientosapol
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - George Sharbeen
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - K K Edwin Lau
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Daniel Bosnjak
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Timothy Durack
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Igor Stevanovski
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Wolfgang Weninger
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Christopher J Jolly
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
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