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Li MWY, Burnett L, Dai P, Avery DT, Noori T, Voskoboinik I, Shah PR, Tatian A, Tangye SG, Gray PE, Ma CS. Filaggrin-Associated Atopic Skin, Eye, Airways, and Gut Disease, Modifying the Presentation of X-Linked Reticular Pigmentary Disorder (XLPDR). J Clin Immunol 2024; 44:38. [PMID: 38165470 DOI: 10.1007/s10875-023-01637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND X-linked reticular pigmentary disorder (XLPDR) is a rare condition characterized by skin hyperpigmentation, ectodermal features, multiorgan inflammation, and recurrent infections. All probands identified to date share the same intronic hemizygous POLA1 hypomorphic variant (NM_001330360.2(POLA1):c.1393-354A > G) on the X chromosome. Previous studies have supported excessive type 1 interferon (IFN) inflammation and natural killer (NK) cell dysfunction in disease pathogenesis. Common null polymorphisms in filaggrin (FLG) gene underlie ichthyosis vulgaris and atopic predisposition. CASE A 9-year-old boy born to non-consanguineous parents developed eczema with reticular skin hyperpigmentation in early infancy. He suffered recurrent chest infections with chronic cough, clubbing, and asthma, moderate allergic rhinoconjunctivitis with keratitis, multiple food allergies, and vomiting with growth failure. Imaging demonstrated bronchiectasis, while gastroscopy identified chronic eosinophilic gastroduodenitis. Interestingly, growth failure and bronchiectasis improved over time without specific treatment. METHODS Whole-genome sequencing (WGS) using Illumina short-read sequencing was followed by both manual and orthogonal automated bioinformatic analyses for single-nucleotide variants, small insertions/deletions (indels), and larger copy number variations. NK cell cytotoxic function was assessed using 51Cr release and degranulation assays. The presence of an interferon signature was investigated using a panel of six interferon-stimulated genes (ISGs) by QPCR. RESULTS WGS identified a de novo hemizygous intronic variant in POLA1 (NM_001330360.2(POLA1):c.1393-354A > G) giving a diagnosis of XLPDR, as well as a heterozygous nonsense FLG variant (NM_002016.2(FLG):c.441del, NP_0020.1:p.(Arg151Glyfs*43)). Compared to healthy controls, the IFN signature was elevated although the degree moderated over time with the improvement in his chest disease. NK cell functional studies showed normal cytotoxicity and degranulation. CONCLUSION This patient had multiple atopic manifestations affecting eye, skin, chest, and gut, complicating the presentation of XLPDR. This highlights that common FLG polymorphisms should always be considered when assessing genotype-phenotype correlations of other genetic variation in patients with atopic symptoms. Additionally, while the patient exhibited an enhanced IFN signature, he does not have an NK cell defect, suggesting this may not be a constant feature of XLPDR.
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Affiliation(s)
- Margaret W Y Li
- Department of Allergy and Immunology, Sydney Children's Hospital, Sydney, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia.
| | - Leslie Burnett
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, St Vincent's Healthcare Clinical Campus, UNSW Sydney, Sydney, Australia
| | - Pei Dai
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
| | | | | | | | - Parth R Shah
- Department of Ophthalmology, Sydney Children's Hospital, Sydney, Australia
| | - Artiene Tatian
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Department of Dermatology, Sydney Children's Hospital, Sydney, Australia
| | - Stuart G Tangye
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
| | - Paul E Gray
- Department of Allergy and Immunology, Sydney Children's Hospital, Sydney, Australia.
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia.
- School of Medicine, Western Sydney University, Sydney, Australia.
| | - Cindy S Ma
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
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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] [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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3
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Van Haute L, O'Connor E, Díaz-Maldonado H, Munro B, Polavarapu K, Hock DH, Arunachal G, Athanasiou-Fragkouli A, Bardhan M, Barth M, Bonneau D, Brunetti-Pierri N, Cappuccio G, Caruana NJ, Dominik N, Goel H, Helman G, Houlden H, Lenaers G, Mention K, Murphy D, Nandeesh B, Olimpio C, Powell CA, Preethish-Kumar V, Procaccio V, Rius R, Rebelo-Guiomar P, Simons C, Vengalil S, Zaki MS, Ziegler A, Thorburn DR, Stroud DA, Maroofian R, Christodoulou J, Gustafsson C, Nalini A, Lochmüller H, Minczuk M, Horvath R. TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease. Nat Commun 2023; 14:1009. [PMID: 36823193 PMCID: PMC9950373 DOI: 10.1038/s41467-023-36277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.
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Affiliation(s)
- Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Héctor Díaz-Maldonado
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Benjamin Munro
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Gautham Arunachal
- Department of Human genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Alkyoni Athanasiou-Fragkouli
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Magalie Barth
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Natalia Dominik
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Himanshu Goel
- Hunter Genetics, Waratah, University of Newcastle, Callaghan, NSW, 2298, Australia
| | - Guy Helman
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Henry Houlden
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Guy Lenaers
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Karine Mention
- Pediatric Inherited Metabolic Disorders, Hôpital Jeanne de Flandre, Lille, France
| | - David Murphy
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Bevinahalli Nandeesh
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Catarina Olimpio
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Vincent Procaccio
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Rocio Rius
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Cas Simons
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Alban Ziegler
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - David R Thorburn
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Reza Maroofian
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Claes Gustafsson
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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4
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Rius R, Bennett NK, Bhattacharya K, Riley LG, Yüksel Z, Formosa LE, Compton AG, Dale RC, Cowley MJ, Gayevskiy V, Al Tala SM, Almehery AA, Ryan MT, Thorburn DR, Nakamura K, Christodoulou J. Biallelic pathogenic variants in COX11 are associated with an infantile-onset mitochondrial encephalopathy. Hum Mutat 2022; 43:1970-1978. [PMID: 36030551 PMCID: PMC9771894 DOI: 10.1002/humu.24453] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/28/2022] [Accepted: 08/22/2022] [Indexed: 01/25/2023]
Abstract
Primary mitochondrial diseases are a group of genetically and clinically heterogeneous disorders resulting from oxidative phosphorylation (OXPHOS) defects. COX11 encodes a copper chaperone that participates in the assembly of complex IV and has not been previously linked to human disease. In a previous study, we identified that COX11 knockdown decreased cellular adenosine triphosphate (ATP) derived from respiration, and that ATP levels could be restored with coenzyme Q10 (CoQ10 ) supplementation. This finding is surprising since COX11 has no known role in CoQ10 biosynthesis. Here, we report a novel gene-disease association by identifying biallelic pathogenic variants in COX11 associated with infantile-onset mitochondrial encephalopathies in two unrelated families using trio genome and exome sequencing. Functional studies showed that mutant COX11 fibroblasts had decreased ATP levels which could be rescued by CoQ10 . These results not only suggest that COX11 variants cause defects in energy production but reveal a potential metabolic therapeutic strategy for patients with COX11 variants.
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Affiliation(s)
- Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - Neal K. Bennett
- Gladstone Institute of Neurological DiseaseGladstone InstitutesSan FranciscoCaliforniaUSA
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders ServiceThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Genetic Medicine, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Lisa G. Riley
- Specialty of Child & Adolescent HealthUniversity of SydneySydneyAustralia
- Rare Diseases Functional GenomicsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Zafer Yüksel
- Department of Human GeneticsBioscientia Healthcare GmbHIngelheimGermany
| | - Luke E. Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Alison G. Compton
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - Russell C. Dale
- Department of Paediatric Neurology and Clinical school, The Children's Hospital at Westmead, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Mark J. Cowley
- Children's Cancer Institute & School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical GenomicsGarvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Saeed M. Al Tala
- Pediatric DirectorateNeonatal NICU, Armed Forces Hospital SRKhamis MushaytSaudi Arabia
| | | | - Michael T. Ryan
- Department of Human GeneticsBioscientia Healthcare GmbHIngelheimGermany
| | - David R. Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
- Victorian Clinical Genetics ServicesRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Ken Nakamura
- Gladstone Institute of Neurological DiseaseGladstone InstitutesSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Graduate Programs in Biomedical Sciences and NeuroscienceUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
- Discipline of Genetic Medicine, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
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Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis. Eur J Hum Genet 2022; 30:1121-1131. [PMID: 35970915 PMCID: PMC9553973 DOI: 10.1038/s41431-022-01162-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/01/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.
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Davis RL, Kumar KR, Puttick C, Liang C, Ahmad KE, Edema-Hildebrand F, Park JS, Minoche AE, Gayevskiy V, Mallawaarachchi AC, Christodoulou J, Schofield D, Dinger ME, Cowley MJ, Sue CM. Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis. Neurology 2022; 99:e730-e742. [PMID: 35641312 PMCID: PMC9484606 DOI: 10.1212/wnl.0000000000200745] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 04/04/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mitochondrial diseases (MDs) are the commonest group of heritable metabolic disorders. Phenotypic diversity can make molecular diagnosis challenging, and causative genetic variants may reside in either mitochondrial or nuclear DNA. A single comprehensive genetic diagnostic test would be highly useful and transform the field. We applied whole-genome sequencing (WGS) to evaluate the variant detection rate and diagnostic capacity of this technology with a view to simplifying and improving the MD diagnostic pathway. METHODS Adult patients presenting to a specialist MD clinic in Sydney, Australia, were recruited to the study if they satisfied clinical MD (Nijmegen) criteria. WGS was performed on blood DNA, followed by clinical genetic analysis for known pathogenic MD-associated variants and MD mimics. RESULTS Of the 242 consecutive patients recruited, 62 participants had "definite," 108 had "probable," and 72 had "possible" MD classification by the Nijmegen criteria. Disease-causing variants were identified for 130 participants, regardless of the location of the causative genetic variants, giving an overall diagnostic rate of 53.7% (130 of 242). Identification of causative genetic variants informed precise treatment, restored reproductive confidence, and optimized clinical management of MD. DISCUSSION Comprehensive bigenomic sequencing accurately detects causative genetic variants in affected MD patients, simplifying diagnosis, enabling early treatment, and informing the risk of genetic transmission.
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Akesson LS, Rius R, Brown NJ, Rosenbaum J, Donoghue S, Stormon M, Chai C, Bordador E, Guo Y, Hakonarson H, Compton AG, Thorburn DR, Amarasekera S, Marum J, Monaco A, Lee C, Chong B, Lunke S, Stark Z, Christodoulou J. Distinct diagnostic trajectories in NBAS-associated acute liver failure highlights the need for timely functional studies. JIMD Rep 2022; 63:240-249. [PMID: 35433172 PMCID: PMC8995841 DOI: 10.1002/jmd2.12280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Variants of uncertain significance (VUS) are commonly found following genomic sequencing, particularly in ethnically diverse populations that are underrepresented in large population databases. Functional characterization of VUS may assist in variant reclassification, however these studies are not readily available and often rely on research funding and good will. We present four individuals from three families at different stages of their diagnostic trajectory with recurrent acute liver failure (RALF) and biallelic NBAS variants, confirmed by either trio analysis or cDNA studies. Functional characterization was undertaken, measuring NBAS and p31 levels by Western blotting, demonstrating reduced NBAS levels in two of three families, and reduced p31 levels in all three families. These results provided functional characterization of the molecular impact of a missense VUS, allowing reclassification of the variant and molecular confirmation of NBAS-associated RALF. Importantly, p31 was decreased in all individuals, including an individual with two missense variants where NBAS protein levels were preserved. These results highlight the importance of access to timely functional studies after identification of putative variants, and the importance of considering a range of assays to validate variants whose pathogenicity is uncertain. We suggest that funding models for genomic sequencing should consider incorporating capabilities for adjunct RNA, protein, biochemical, and other specialized tests to increase the diagnostic yield which will lead to improved medical care, increased equity, and access to molecular diagnoses for all patients.
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Affiliation(s)
- Lauren S. Akesson
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- SA PathologySA HealthAdelaideSAAustralia
- School of Biomedicine, Faculty of Medicine, Dentistry and Health SciencesUniversity of AdelaideAdelaideAustraliaAustralia
| | - Rocio Rius
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Natasha J. Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Jeremy Rosenbaum
- Department of GastroenterologyRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Sarah Donoghue
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Michael Stormon
- Department of GastroenterologyChildren's Hospital WestmeadSydneyNew South WalesAustralia
- Discipline of Child & Adolescent Health, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Charmaine Chai
- Department of GastroenterologyChildren's Hospital WestmeadSydneyNew South WalesAustralia
| | - Esmeralda Bordador
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Yiran Guo
- Center for Applied GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Center for Data‐Driven Discovery in BiomedicineChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Hakon Hakonarson
- Center for Applied GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of Pediatrics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Alison G. Compton
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - David R. Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Sumudu Amarasekera
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Alisha Monaco
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PathologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Brain and Mitochondrial Research GroupMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
- Discipline of Child & Adolescent Health, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
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8
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Rudaks LI, Watson E, Oboudiyat C, Kumar KR, Sullivan P, Cowley MJ, Davis RL, Sue CM. Decompensation of cardiorespiratory function and emergence of anemia during pregnancy in a case of mitochondrial myopathy, lactic acidosis, and sideroblastic anemia 2 with compound heterozygous YARS2 pathogenic variants. Am J Med Genet A 2022; 188:2226-2230. [PMID: 35393742 PMCID: PMC9541592 DOI: 10.1002/ajmg.a.62755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/01/2022] [Accepted: 03/13/2022] [Indexed: 12/03/2022]
Abstract
Myopathy, lactic acidosis, and sideroblastic anemia 2 (MLASA2) is an autosomal recessive mitochondrial disorder caused by pathogenic variants in YARS2. YARS2 variants confer heterogeneous phenotypes ranging from the full MLASA syndrome to a clinically unaffected state. Symptom onset is most common in the first decade of life but can occur in adulthood and has been reported following intercurrent illness. Early death can result from respiratory muscle weakness and cardiomyopathy. We report a case of MLASA2 with compound heterozygous YARS2 pathogenic variants; a known pathogenic nonsense variant [NM_001040436.3:c.98C>A (p.Ser33Ter)] and a likely pathogenic missense variant not previously associated with disease [NM_001040436.3:c.948G>T (p.Arg316Ser)]. The proband initially presented with a relatively mild phenotype of myopathy and lactic acidosis. During pregnancy, anemia emerged as an additional feature and in the postpartum period she experienced severe decompensation of cardiorespiratory function. This is the first reported case of pregnancy‐related complications in a patient with YARS2‐related mitochondrial disease. This case highlights the need for caution and careful counseling when considering pregnancy in mitochondrial disease, due to the risk of disease exacerbation and pregnancy complications.
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Affiliation(s)
- Laura I Rudaks
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Eloise Watson
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Carly Oboudiyat
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Kishore R Kumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales, Australia.,Translational Genome Informatics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ryan L Davis
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Translational Genome Informatics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Kolling Institute, Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales, Australia
| | - Carolyn M Sue
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Translational Genome Informatics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Kolling Institute, Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, New South Wales, Australia
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9
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Mallawaarachchi AC, Lundie B, Hort Y, Schonrock N, Senum SR, Gayevskiy V, Minoche AE, Hollway G, Ohnesorg T, Hinchcliffe M, Patel C, Tchan M, Mallett A, Dinger ME, Rangan G, Cowley MJ, Harris PC, Burnett L, Shine J, Furlong TJ. Genomic diagnostics in polycystic kidney disease: an assessment of real-world use of whole-genome sequencing. Eur J Hum Genet 2021; 29:760-770. [PMID: 33437033 PMCID: PMC8110527 DOI: 10.1038/s41431-020-00796-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/03/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is common, with a prevalence of 1/1000 and predominantly caused by disease-causing variants in PKD1 or PKD2. Clinical diagnosis is usually by age-dependent imaging criteria, which is challenging in patients with atypical clinical features, without family history, or younger age. However, there is increasing need for definitive diagnosis of ADPKD with new treatments available. Sequencing is complicated by six pseudogenes that share 97% homology to PKD1 and by recently identified phenocopy genes. Whole-genome sequencing can definitively diagnose ADPKD, but requires validation for clinical use. We initially performed a validation study, in which 42 ADPKD patients underwent sequencing of PKD1 and PKD2 by both whole-genome and Sanger sequencing, using a blinded, cross-over method. Whole-genome sequencing identified all PKD1 and PKD2 germline pathogenic variants in the validation study (sensitivity and specificity 100%). Two mosaic variants outside pipeline thresholds were not detected. We then examined the first 144 samples referred to a clinically-accredited diagnostic laboratory for clinical whole-genome sequencing, with targeted-analysis to a polycystic kidney disease gene-panel. In this unselected, diagnostic cohort (71 males :73 females), the diagnostic rate was 70%, including a diagnostic rate of 81% in patients with typical ADPKD (98% with PKD1/PKD2 variants) and 60% in those with atypical features (56% PKD1/PKD2; 44% PKHD1/HNF1B/GANAB/ DNAJB11/PRKCSH/TSC2). Most patients with atypical disease did not have clinical features that predicted likelihood of a genetic diagnosis. These results suggest clinicians should consider diagnostic genomics as part of their assessment in polycystic kidney disease, particularly in atypical disease.
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Affiliation(s)
- Amali C. Mallawaarachchi
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW Australia ,Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW Australia ,Genome.One, Sydney, NSW Australia
| | | | - Yvonne Hort
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Nicole Schonrock
- Genome.One, Sydney, NSW Australia ,Garvan Institute of Medical Research, Sydney, NSW Australia ,St Vincent’s Hospital Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Sarah R. Senum
- Division of Nephrology and Hypertension, The Mayo Clinic, Rochester, MN USA
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Georgina Hollway
- Genome.One, Sydney, NSW Australia ,Garvan Institute of Medical Research, Sydney, NSW Australia ,St Vincent’s Hospital Clinical School, University of New South Wales, Sydney, NSW Australia
| | | | | | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD Australia
| | - Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney, NSW Australia ,Sydney Medical School, The University of Sydney, Sydney, NSW Australia
| | - Andrew Mallett
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD Australia ,Institute for Molecular Bioscience & Faculty of Medicine, The University of Queensland, Brisbane, QLD Australia ,KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, VIC Australia
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW Australia
| | - Gopala Rangan
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW Australia ,Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW Australia
| | - Mark J. Cowley
- Garvan Institute of Medical Research, Sydney, NSW Australia ,St Vincent’s Hospital Clinical School, University of New South Wales, Sydney, NSW Australia ,Children’s Cancer Institute, Sydney, NSW Australia
| | - Peter C. Harris
- Division of Nephrology and Hypertension, The Mayo Clinic, Rochester, MN USA
| | - Leslie Burnett
- Genome.One, Sydney, NSW Australia ,St Vincent’s Hospital Clinical School, University of New South Wales, Sydney, NSW Australia ,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW Australia ,Sydney Medical School, The University of Sydney, Sydney, NSW Australia
| | - John Shine
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Timothy J. Furlong
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW Australia ,Department of Renal Medicine, St Vincent’s Hospital, Sydney, NSW Australia
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10
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Rius R, Compton AG, Baker NL, Welch AE, Coman D, Kava MP, Minoche AE, Cowley MJ, Thorburn DR, Christodoulou J. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. Genes (Basel) 2021; 12:genes12040607. [PMID: 33924034 PMCID: PMC8072654 DOI: 10.3390/genes12040607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related costs and challenges in data analysis. In this article, we report three patients with mitochondrial disease molecularly diagnosed through GS performed on DNA extracted from blood to demonstrate different diagnostic advantages of this technology, including the detection of a low-level heteroplasmic pathogenic variant, an intragenic nuclear DNA deletion, and a large mtDNA deletion. Current technical improvements and cost reductions are likely to lead to an expanded routine diagnostic usage of GS and of the complementary “Omic” technologies in mitochondrial diseases.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Naomi L. Baker
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - AnneMarie E. Welch
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
| | - David Coman
- Department of Metabolic Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia;
- School of Clinical Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- School of Medicine, Griffith University, Gold Coast, QLD 4222, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia;
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +61-39936-6353
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11
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Palmer EE, Sachdev R, Macintosh R, Melo US, Mundlos S, Righetti S, Kandula T, Minoche AE, Puttick C, Gayevskiy V, Hesson L, Idrisoglu S, Shoubridge C, Thai MHN, Davis RL, Drew AP, Sampaio H, Andrews PI, Lawson J, Cardamone M, Mowat D, Colley A, Kummerfeld S, Dinger ME, Cowley MJ, Roscioli T, Bye A, Kirk E. Diagnostic Yield of Whole Genome Sequencing After Nondiagnostic Exome Sequencing or Gene Panel in Developmental and Epileptic Encephalopathies. Neurology 2021; 96:e1770-e1782. [PMID: 33568551 DOI: 10.1212/wnl.0000000000011655] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE). METHODS We performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray and either research ES (n = 15) or diagnostic MGP (n = 15). RESULTS Eight diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants, which now had additional evidence for pathogenicity. Eleven diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n = 10) involved genes not included in the panel, particularly in individuals with postneonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features, or multiorgan involvement. A total of 42% of diagnoses were autosomal recessive or X-chromosome linked. CONCLUSION WGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n = 3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel noncoding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.
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Affiliation(s)
- Elizabeth Emma Palmer
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia.
| | - Rani Sachdev
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Rebecca Macintosh
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Uirá Souto Melo
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Stefan Mundlos
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Righetti
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tejaswi Kandula
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Andre E Minoche
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Clare Puttick
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Velimir Gayevskiy
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Luke Hesson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Senel Idrisoglu
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Cheryl Shoubridge
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Monica Hong Ngoc Thai
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ryan L Davis
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alexander P Drew
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Hugo Sampaio
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Peter Ian Andrews
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - John Lawson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Michael Cardamone
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - David Mowat
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alison Colley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Kummerfeld
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Marcel E Dinger
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Mark J Cowley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tony Roscioli
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ann Bye
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Edwin Kirk
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
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12
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Khuong-Quang DA, Brown LM, Wong M, Mayoh C, Sexton-Oates A, Kumar A, Pinese M, Nagabushan S, Lau L, Ludlow LE, Gifford AJ, Rodriguez M, Desai J, Fox SB, Haber M, Ziegler DS, Hansford JR, Marshall GM, Cowley MJ, Ekert PG. Recurrent SPECC1L-NTRK fusions in pediatric sarcoma and brain tumors. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005710. [PMID: 33144287 PMCID: PMC7784491 DOI: 10.1101/mcs.a005710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/22/2020] [Indexed: 12/02/2022] Open
Abstract
The identification of rearrangements driving expression of neurotrophic receptor tyrosine kinase (NTRK) family kinases in tumors has become critically important because of the availability of effective, specific inhibitor drugs. Whole-genome sequencing (WGS) combined with RNA sequencing (RNA-seq) can identify novel and recurrent expressed fusions. Here we describe three SPECC1L–NTRK fusions identified in two pediatric central nervous system cancers and an extracranial solid tumor using WGS and RNA-seq. These fusions arose either through a simple balanced rearrangement or in the context of a complex chromoplexy event. We cloned the SPECC1L–NTRK2 fusion directly from a patient sample and showed that enforced expression of this fusion is sufficient to promote cytokine-independent survival and proliferation. Cells transformed by SPECC1L–NTRK2 expression are sensitive to a TRK inhibitor drug. We report here that SPECC1L–NTRK fusions can arise in a range of pediatric cancers. Although WGS and RNA-seq are not required to detect NTRK fusions, these techniques may be of benefit when NTRK fusions are not suspected on clinical grounds or not identified by other methods.
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Affiliation(s)
- Dong-Anh Khuong-Quang
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Children's Cancer Centre, Royal Children's Hospital, Parkville, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Lauren M Brown
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,Department of Pediatrics, University of Melbourne, Parkville, 3052, Australia
| | - Marie Wong
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - Alexandra Sexton-Oates
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Amit Kumar
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Mark Pinese
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - Sumanth Nagabushan
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Loretta Lau
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Louise E Ludlow
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, 2031, Australia
| | - Michael Rodriguez
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, 2031, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, 3000, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, University of Melbourne, 3000, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Michelle Haber
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia
| | - David S Ziegler
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Parkville, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,Department of Pediatrics, University of Melbourne, Parkville, 3052, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia
| | - Paul G Ekert
- Children's Cancer Institute, University of New South Wales, Randwick, 2031, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Australia.,School of Women's and Children's Health, UNSW Medicine, UNSW Sydney, Randwick, 2031, Australia.,Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
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13
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Comprehensive Mutational and Phenotypic Characterization of New Metastatic Cutaneous Squamous Cell Carcinoma Cell Lines Reveal Novel Drug Susceptibilities. Int J Mol Sci 2020; 21:ijms21249536. [PMID: 33333825 PMCID: PMC7765308 DOI: 10.3390/ijms21249536] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer. Most patients who develop metastases (2–5%) present with advanced disease that requires a combination of radical surgery and adjuvant radiation therapy. There are few effective therapies for refractory disease. In this study, we describe novel patient-derived cell lines from cSCC metastases of the head and neck (designated UW-CSCC1 and UW-CSCC2). The cell lines genotypically and phenotypically resembled the original patient tumor and were tumorogenic in mice. Differences in cancer-related gene expression between the tumor and cell lines after various culturing conditions could be largely reversed by xenografting and reculturing. The novel drug susceptibilities of UW-CSCC1 and an irradiated subclone UW-CSCC1-R to drugs targeting cell cycle, PI3K/AKT/mTOR, and DNA damage pathways were observed using high-throughput anti-cancer and kinase-inhibitor compound libraries, which correlate with either copy number variations, targetable mutations and/or the upregulation of gene expression. A secondary screen of top hits in all three cell lines including PIK3CA-targeting drugs supports the utility of targeting the PI3K/AKT/mTOR pathway in this disease. UW-CSCC cell lines are thus useful preclinical models for determining targetable pathways and candidate therapeutics.
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14
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Wong M, Mayoh C, Lau LMS, Khuong-Quang DA, Pinese M, Kumar A, Barahona P, Wilkie EE, Sullivan P, Bowen-James R, Syed M, Martincorena I, Abascal F, Sherstyuk A, Bolanos NA, Baber J, Priestley P, Dolman MEM, Fleuren EDG, Gauthier ME, Mould EVA, Gayevskiy V, Gifford AJ, Grebert-Wade D, Strong PA, Manouvrier E, Warby M, Thomas DM, Kirk J, Tucker K, O'Brien T, Alvaro F, McCowage GB, Dalla-Pozza L, Gottardo NG, Tapp H, Wood P, Khaw SL, Hansford JR, Moore AS, Norris MD, Trahair TN, Lock RB, Tyrrell V, Haber M, Marshall GM, Ziegler DS, Ekert PG, Cowley MJ. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nat Med 2020; 26:1742-1753. [PMID: 33020650 DOI: 10.1038/s41591-020-1072-4] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023]
Abstract
The Zero Childhood Cancer Program is a precision medicine program to benefit children with poor-outcome, rare, relapsed or refractory cancer. Using tumor and germline whole genome sequencing (WGS) and RNA sequencing (RNAseq) across 252 tumors from high-risk pediatric patients with cancer, we identified 968 reportable molecular aberrations (39.9% in WGS and RNAseq, 35.1% in WGS only and 25.0% in RNAseq only). Of these patients, 93.7% had at least one germline or somatic aberration, 71.4% had therapeutic targets and 5.2% had a change in diagnosis. WGS identified pathogenic cancer-predisposing variants in 16.2% of patients. In 76 central nervous system tumors, methylome analysis confirmed diagnosis in 71.1% of patients and contributed to a change of diagnosis in two patients (2.6%). To date, 43 patients have received a recommended therapy, 38 of whom could be evaluated, with 31% showing objective evidence of clinical benefit. Comprehensive molecular profiling resolved the molecular basis of virtually all high-risk cancers, leading to clinical benefit in some patients.
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Affiliation(s)
- Marie Wong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Loretta M S Lau
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Amit Kumar
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Paulette Barahona
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emilie E Wilkie
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Rachel Bowen-James
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Mustafa Syed
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | | | | | - Alexandra Sherstyuk
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Noemi A Bolanos
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Peter Priestley
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - M Emmy M Dolman
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Marie-Emilie Gauthier
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Emily V A Mould
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Dylan Grebert-Wade
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Patrick A Strong
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Elodie Manouvrier
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Meera Warby
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - David M Thomas
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Katherine Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, Australia
- Prince of Wales Hospital Clinical School, University of New South Wales, Randwick, NSW, Australia
| | - Tracey O'Brien
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Frank Alvaro
- John Hunter Children's Hospital, New Lambton Heights, NSW, Australia
| | - Geoffry B McCowage
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - Luciano Dalla-Pozza
- Cancer Centre for Children, The Children's Hospital Westmead, Westmead, NSW, Australia
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital, Nedlands, WA, Australia
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | - Heather Tapp
- Women's and Children's Hospital, Adelaide, SA, Australia
| | - Paul Wood
- Monash Children's Hospital, Melbourne, VIC, Australia
| | - Seong-Lin Khaw
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
| | - Andrew S Moore
- Oncology Service, Oncology Service, Queensland Children's Hospital, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Toby N Trahair
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
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15
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Martin PB, Kigoshi-Tansho Y, Sher RB, Ravenscroft G, Stauffer JE, Kumar R, Yonashiro R, Müller T, Griffith C, Allen W, Pehlivan D, Harel T, Zenker M, Howting D, Schanze D, Faqeih EA, Almontashiri NAM, Maroofian R, Houlden H, Mazaheri N, Galehdari H, Douglas G, Posey JE, Ryan M, Lupski JR, Laing NG, Joazeiro CAP, Cox GA. NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease. Nat Commun 2020; 11:4625. [PMID: 32934225 PMCID: PMC7494853 DOI: 10.1038/s41467-020-18327-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
A hallmark of neurodegeneration is defective protein quality control. The E3 ligase Listerin (LTN1/Ltn1) acts in a specialized protein quality control pathway—Ribosome-associated Quality Control (RQC)—by mediating proteolytic targeting of incomplete polypeptides produced by ribosome stalling, and Ltn1 mutation leads to neurodegeneration in mice. Whether neurodegeneration results from defective RQC and whether defective RQC contributes to human disease have remained unknown. Here we show that three independently-generated mouse models with mutations in a different component of the RQC complex, NEMF/Rqc2, develop progressive motor neuron degeneration. Equivalent mutations in yeast Rqc2 selectively interfere with its ability to modify aberrant translation products with C-terminal tails which assist with RQC-mediated protein degradation, suggesting a pathomechanism. Finally, we identify NEMF mutations expected to interfere with function in patients from seven families presenting juvenile neuromuscular disease. These uncover NEMF’s role in translational homeostasis in the nervous system and implicate RQC dysfunction in causing neurodegeneration. Defective protein quality control is a key feature of neurodegeneration. Here, the authors show that mutations in Nemf/NEMF, a component of the Ribosome-associated Quality Control complex, have a neurodegenerative effect in mice and may underlie neuromuscular disease in seven unrelated families.
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Affiliation(s)
- Paige B Martin
- The Jackson Laboratory, Bar Harbor, ME, USA.,The University of Maine, Graduate School of Biomedical Science and Engineering, Orono, ME, USA
| | - Yu Kigoshi-Tansho
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Roger B Sher
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY, USA.,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, USA
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | | | - Rajesh Kumar
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ryo Yonashiro
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Tina Müller
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | | | - William Allen
- Mission Fullerton Genetics Center, Mission Health, Asheville, NC, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Denise Howting
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Denny Schanze
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Eissa A Faqeih
- Department of Genetics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Naif A M Almontashiri
- The Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia.,Faculty of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Reza Maroofian
- Neurogenetics Laboratory, UCL Queen Square Institute of Neurology, London, UK.,The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neurogenetics Laboratory, UCL Queen Square Institute of Neurology, London, UK.,The National Hospital for Neurology and Neurosurgery, London, UK
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Monique Ryan
- Department of Neurology, The Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute and University of Melbourne, Melbourne, VIC, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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16
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Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M, Lake NJ, Tregoning S, Jabbari JS, Lucattini A, Nitta KR, Ohtake A, Murayama K, Amor DJ, McGillivray G, Wong FY, van der Knaap MS, Jeroen Vermeulen R, Wiltshire EJ, Fletcher JM, Lewis B, Baynam G, Ellaway C, Balasubramaniam S, Bhattacharya K, Freckmann ML, Arbuckle S, Rodriguez M, Taft RJ, Sadedin S, Cowley MJ, Minoche AE, Calvo SE, Mootha VK, Ryan MT, Okazaki Y, Stroud DA, Simons C, Christodoulou J, Thorburn DR. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. MED 2020; 2:49-73. [PMID: 33575671 DOI: 10.1016/j.medj.2020.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.
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Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Alison G Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Daniella H Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - AnneMarie E Welch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.,Division of Genomic Medicine Research, Medical Genomics Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Min Wang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nicole J Lake
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Simone Tregoning
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University Hospital, Saitama, 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flora Y Wong
- Ritchie Centre, Hudson Institute of Medical Research; Department of Paediatrics, Monash University; and Monash Newborn, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Marjo S van der Knaap
- Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands
| | - R Jeroen Vermeulen
- Department of Neurology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | - Esko J Wiltshire
- Department of Paediatrics and Child Health, University of Otago Wellington and Capital and Coast District Health Board, Wellington 6021, New Zealand
| | - Janice M Fletcher
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Barry Lewis
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and King Edward Memorial Hospital for Women Perth, Subiaco, WA 6008, Australia.,Telethon Kids Institute and School of Paediatrics and Child Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | | | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW 2145, Australia
| | - Michael Rodriguez
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Simon Sadedin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Kensington, NSW 2750, Australia; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Lead contact
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17
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The diagnostic utility of genome sequencing in a pediatric cohort with suspected mitochondrial disease. Genet Med 2020; 22:1254-1261. [DOI: 10.1038/s41436-020-0793-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/15/2022] Open
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18
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McCabe MJ, Gauthier MEA, Chan CL, Thompson TJ, De Sousa SMC, Puttick C, Grady JP, Gayevskiy V, Tao J, Ying K, Cipponi A, Deng N, Swarbrick A, Thomas ML, Lord RV, Johns AL, Kohonen-Corish M, O'Toole SA, Clark J, Mueller SA, Gupta R, McCormack AI, Dinger ME, Cowley MJ. Development and validation of a targeted gene sequencing panel for application to disparate cancers. Sci Rep 2019; 9:17052. [PMID: 31745186 PMCID: PMC6864073 DOI: 10.1038/s41598-019-52000-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.
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Affiliation(s)
- Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
| | - Marie-Emilie A Gauthier
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Children's Cancer Institute, Randwick, NSW, Australia
| | - Chia-Ling Chan
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Tanya J Thompson
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Clare Puttick
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John P Grady
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Arcadi Cipponi
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Niantao Deng
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Alex Swarbrick
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Melissa L Thomas
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Reginald V Lord
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- Notre Dame University School of Medicine, Sydney, NSW, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Maija Kohonen-Corish
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St George and Sutherland Clinical School, UNSW Australia, Sydney, NSW, Australia
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Sandra A O'Toole
- Northern Clinical School, The University of Sydney, Royal North Shore Hospital, St Leonards, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown,, NSW, Australia
- Western Sydney University Medical School, Campbelltown, NSW, Australia
- Australian Clinical Labs, Bella Vista, NSW, Australia
| | - Jonathan Clark
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Simon A Mueller
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department for Oto-Rhino-Laryngology, Head and Neck Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ruta Gupta
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Ann I McCormack
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
- Department of Endocrinology, St Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia.
- Children's Cancer Institute, Randwick, NSW, Australia.
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19
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Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon. Genet Med 2019; 21:2823-2826. [PMID: 31171843 DOI: 10.1038/s41436-019-0568-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/24/2019] [Indexed: 01/07/2023] Open
Abstract
PURPOSE A recent report has raised the possibility of biparental mitochondrial DNA (mtDNA) inheritance, which could lead to concerns by health-care professionals and patients regarding investigations and genetic counseling of families with pathogenic mitochondrial DNA variants. Our aim was to examine the frequency of this phenomenon by investigating a cohort of patients with suspected mitochondrial disease. METHODS We studied genome sequencing (GS) data of DNA extracted from blood samples of 41 pediatric patients with suspected mitochondrial disease and their parents. RESULTS All of the mtDNA variants in the probands segregated with their mother or were apparently de novo. There were no variants that segregated only with the father and none of these families showed evidence of biparental inheritance of their mtDNA. CONCLUSION Paternal mitochondrial transmission is unlikely to be a common occurrence and therefore at this point we would not recommend changes in clinical practice.
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20
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Kang C, Liang C, Ahmad KE, Gu Y, Siow SF, Colebatch JG, Whyte S, Ng K, Cremer PD, Corbett AJ, Davis RL, Roscioli T, Cowley MJ, Park JS, Sue CM, Kumar KR. High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia. THE CEREBELLUM 2019; 18:137-146. [PMID: 30078120 DOI: 10.1007/s12311-018-0969-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic testing strategies such as next-generation sequencing (NGS) panels and whole genome sequencing (WGS) can be applied to the hereditary cerebellar ataxias (HCAs), but their exact role in the diagnostic pathway is unclear. We aim to determine the yield from genetic testing strategies and the genetic and phenotypic spectrum of HCA in Australia by analysing real-world data. We performed a retrospective review on 87 HCA cases referred to the Neurogenetics Clinic at the Royal North Shore Hospital, Sydney, Australia. Probands underwent triplet repeat expansion testing; those that tested negative had NGS-targeted panels and WGS testing when available. In our sample, 58.6% were male (51/87), with an average age at onset of 37.1 years. Individuals with sequencing variants had a prolonged duration of illness compared to those with a triplet repeat expansion. The detection rate in probands for routine repeat expansion panels was 13.8% (11/80). NGS-targeted panels yielded a further 11 individuals (11/32, 34.4%), with WGS yielding 1 more diagnosis (1/3, 33.3%). NGS panels and WGS improved the overall diagnostic rate to 28.8% (23/80) in 14 known HCA loci. The genetic findings included novel variants in ANO10, CACNA1A, PRKCG and SPG7. Our findings highlight the genetic heterogeneity of HCAs and support the use of NGS approaches for individuals who were negative on repeat expansion testing. In comparison to repeat disorders, individuals with sequencing variants may have a prolonged duration of illness, consistent with slower progression of disease.
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Affiliation(s)
- Ce Kang
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia
| | - Christina Liang
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kate E Ahmad
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Yufan Gu
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Sue-Faye Siow
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - James G Colebatch
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, Australia
| | - Scott Whyte
- Department of Neurology, Gosford Hospital, Gosford, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Philip D Cremer
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Alastair J Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, Australia
| | - Ryan L Davis
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia.,Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia
| | - Tony Roscioli
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Department of Clinical Genetics, Sydney Children's Hospital, Randwick, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Jin-Sung Park
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Experimental Animal Research, Seoul National University Hospital, Biomedical Research Institute, Seoul, Republic of Korea
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia. .,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia. .,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
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21
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Increased Diagnostic Yield of Spastic Paraplegia with or Without Cerebellar Ataxia Through Whole-Genome Sequencing. THE CEREBELLUM 2019; 18:781-790. [DOI: 10.1007/s12311-019-01038-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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22
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McCabe MJ, Pinese M, Chan CL, Sheriff N, Thompson TJ, Grady J, Wong M, Gauthier MEA, Puttick C, Gayevskiy V, Hajdu E, Wong SQ, Barrett W, Earls P, Lukeis R, Cheng YY, Lin RCY, Thomas DM, Watkins DN, Dinger ME, McCormack AI, Cowley MJ. Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003764. [PMID: 30936196 PMCID: PMC6549567 DOI: 10.1101/mcs.a003764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/11/2019] [Indexed: 12/22/2022] Open
Abstract
Adrenocortical carcinoma is a rare malignancy with a poor prognosis and few treatment options. Molecular characterization of this cancer remains limited. We present a case of an adrenocortical carcinoma (ACC) in a 37-yr-old female, with dual lung metastases identified 1 yr following commencement of adjuvant mitotane therapy. As standard therapeutic regimens are often unsuccessful in ACC, we undertook a comprehensive genomic study into this case to identify treatment options and monitor disease progress. We performed targeted and whole-genome sequencing of germline, primary tumor, and both metastatic tumors from this patient and monitored recurrence over 2 years using liquid biopsy for ctDNA and steroid hormone measurements. Sequencing revealed the primary and metastatic tumors were hyperhaploid, with extensive loss of heterozygosity but few structural rearrangements. Loss-of-function mutations were identified in MSH2, TP53, RB1, and PTEN, resulting in tumors with mismatch repair signatures and microsatellite instability. At the cellular level, tumors were populated by mitochondria-rich oncocytes. Longitudinal ctDNA mutation and hormone profiles were unable to detect micrometastatic disease, consistent with clinical indicators of disease remission. The molecular signatures in our ACC case suggested immunotherapy in the event of disease progression; however, the patient remains free of cancer. The extensive molecular analysis presented here could be applied to other rare and/or poorly stratified cancers to identify novel or repurpose existing therapeutic options, thereby broadly improving diagnoses, treatments, and prognoses.
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Affiliation(s)
- Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia
| | - Mark Pinese
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Chia-Ling Chan
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Nisa Sheriff
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Department of Endocrinology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Tanya J Thompson
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - John Grady
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marie Wong
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marie-Emilie A Gauthier
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Clare Puttick
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Elektra Hajdu
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Stephen Q Wong
- Molecular and Translational Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Wade Barrett
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Peter Earls
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Robyn Lukeis
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Yuen Y Cheng
- Asbestos Diseases Research Institute, The University of Sydney, Sydney, New South Wales 2139, Australia
| | - Ruby C Y Lin
- Asbestos Diseases Research Institute, The University of Sydney, Sydney, New South Wales 2139, Australia.,Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, New South Wales 2145, Australia
| | - David M Thomas
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - D Neil Watkins
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia
| | - Ann I McCormack
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia.,Department of Endocrinology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia.,Computational Biology Group, Children's Cancer Institute, Kensington, New South Wales 2031, Australia
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23
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Leong TL, Gayevskiy V, Steinfort DP, De Massy MR, Gonzalez-Rajal A, Marini KD, Stone E, Chin V, Havryk A, Plit M, Irving LB, Jennings BR, McCloy RA, Jayasekara WSN, Alamgeer M, Boolell V, Field A, Russell PA, Kumar B, Gough DJ, Szczepny A, Ganju V, Rossello FJ, Cain JE, Papenfuss AT, Asselin-Labat ML, Cowley MJ, Watkins DN. Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer. Oncogene 2019; 38:1661-1675. [PMID: 30348992 PMCID: PMC6462862 DOI: 10.1038/s41388-018-0536-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/13/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic heterogeneity in lung cancer is largely based on the analysis of early-stage surgical specimens. Here we used endoscopic sampling of paired primary and intrathoracic metastatic tumors from 11 lung cancer patients to map genomic heterogeneity inoperable lung cancer with deep whole-genome sequencing. Intra-patient heterogeneity in driver or targetable mutations was predominantly in the form of copy number gain. Private mutation signatures, including patterns consistent with defects in homologous recombination, were highly variable both within and between patients. Irrespective of histotype, we observed a smaller than expected number of private mutations, suggesting that ancestral clones accumulated large mutation burdens immediately prior to metastasis. Single-region whole-genome sequencing of from 20 patients showed that tumors in ever-smokers with the strongest tobacco signatures were associated with germline variants in genes implicated in the repair of cigarette-induced DNA damage. Our results suggest that lung cancer precursors in ever-smokers accumulate large numbers of mutations prior to the formation of frank malignancy followed by rapid metastatic spread. In advanced lung cancer, germline variants in DNA repair genes may interact with the airway environment to influence the pattern of founder mutations, whereas similar interactions with the tumor microenvironment may play a role in the acquisition of mutations following metastasis.
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Affiliation(s)
- Tracy L Leong
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Velimir Gayevskiy
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Daniel P Steinfort
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3050, Australia
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
| | - Marc R De Massy
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Alvaro Gonzalez-Rajal
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Kieren D Marini
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Emily Stone
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Venessa Chin
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
- Department of Medical Oncology, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Adrian Havryk
- Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
| | - Marshall Plit
- Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
| | - Louis B Irving
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3050, Australia
- Department of Respiratory Medicine, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
| | - Barton R Jennings
- Department of Respiratory and Sleep Medicine, Monash Health, Clayton, VIC, 3168, Australia
| | - Rachael A McCloy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - Muhammad Alamgeer
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Vishal Boolell
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Andrew Field
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
- Department of Pathology, St Vincent's Hospital, Sydney, NSW, 2010, Australia
| | - Prudence A Russell
- Department of Pathology, St Vincent's Hospital Melbourne, Fitzroy, VIC, 3000, Australia
| | - Beena Kumar
- Department of Pathology, Monash Health, Clayton, VIC, 3168, Australia
| | - Daniel J Gough
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Anette Szczepny
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Vinod Ganju
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3168, Australia
| | - Jason E Cain
- The Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Anthony T Papenfuss
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3052, Australia
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Marie-Liesse Asselin-Labat
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3050, Australia.
| | - Mark J Cowley
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia.
- Children's Cancer Institute, Kensington, NSW, 2750, Australia.
| | - D Neil Watkins
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia.
- Department of Medical Oncology, St Vincent's Hospital, Darlinghurst, NSW, 2010, Australia.
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24
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Cowley MJ, Liu YC, Oliver KL, Carvill G, Myers CT, Gayevskiy V, Delatycki M, Vlaskamp DRM, Zhu Y, Mefford H, Buckley MF, Bahlo M, Scheffer IE, Dinger ME, Roscioli T. Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection. Hum Mutat 2019; 40:374-379. [PMID: 30556619 PMCID: PMC6492103 DOI: 10.1002/humu.23699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022]
Abstract
Rapid advances in genomic technologies have facilitated the identification pathogenic variants causing human disease. We report siblings with developmental and epileptic encephalopathy due to a novel, shared heterozygous pathogenic 13 bp duplication in SYNGAP1 (c.435_447dup, p.(L150Vfs*6)) that was identified by whole genome sequencing (WGS). The pathogenic variant had escaped earlier detection via two methodologies: whole exome sequencing and high-depth targeted sequencing. Both technologies had produced reads carrying the variant, however, they were either not aligned due to the size of the insertion or aligned to multiple major histocompatibility complex (MHC) regions in the hg19 reference genome, making the critical reads unavailable for variant calling. The WGS pipeline followed different protocols, including alignment of reads to the GRCh37 reference genome, which lacks the additional MHC contigs. Our findings highlight the benefit of using orthogonal clinical bioinformatic pipelines and all relevant inheritance patterns to re-analyze genomic data in undiagnosed patients.
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Affiliation(s)
- Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Yu-Chi Liu
- Population Health and Immunity Division, Walter and Eliza Hall Institute, Melbourne, Australia.,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Karen L Oliver
- Population Health and Immunity Division, Walter and Eliza Hall Institute, Melbourne, Australia.,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Gemma Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Candace T Myers
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - Danique R M Vlaskamp
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Ying Zhu
- Department of Medical Genetics, Royal North Shore Hospital, St Leonards, Australia
| | - Heather Mefford
- Department of Pediatrics, University of Washington, Seattle, WA
| | | | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute, Melbourne, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia.,Florey Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, Australia.,Neuroscience Research Australia, University of New South Wales, Randwick, Sydney, Australia
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25
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Kumar KR, Wali G, Davis RL, Mallawaarachchi AC, Palmer EE, Gayevskiy V, Minoche AE, Veivers D, Dinger ME, Mackay-Sim A, Cowley MJ, Sue CM. Expanding the spectrum of PEX16 mutations and novel insights into disease mechanisms. Mol Genet Metab Rep 2018; 16:46-51. [PMID: 30094183 PMCID: PMC6072801 DOI: 10.1016/j.ymgmr.2018.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 02/04/2023] Open
Abstract
Zellweger syndrome spectrum disorders are caused by mutations in any of at least 12 different PEX genes. This includes PEX16, an important regulator of peroxisome biogenesis. Using whole genome sequencing, we detected previously unreported, biallelic variants in PEX16 [NM_004813.2:c.658G>A, p.(Ala220Thr) and NM_004813.2:c.830G>A, p.(Arg277Gln)] in an individual with leukodystrophy, spastic paraplegia, cerebellar ataxia, and craniocervical dystonia with normal plasma very long chain fatty acids. Using olfactory-neurosphere derived cells, a population of neural stem cells, we showed patient cells had reduced peroxisome density and increased peroxisome size, replicating previously reported findings in PEX16 cell lines. Along with alterations in peroxisome morphology, patient cells also had impaired peroxisome function with reduced catalase activity. Furthermore, patient cells had reduced oxidative stress levels after exposure to hydrogen-peroxide (H2O2), which may be a result of compensation by H2O2 metabolising enzymes other than catalase to preserve peroxisome-related cell functions. Our findings of impaired catalase activity and altered oxidative stress response are novel. Our study expands the phenotype of PEX16 mutations by including dystonia and provides further insights into the pathological mechanisms underlying PEX16-associated disorders. Additional studies of the full spectrum of peroxisomal dysfunction could improve our understanding of the mechanism underlying PEX16-associated disorders.
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Affiliation(s)
- Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | - Gautam Wali
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | - Ryan L. Davis
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | | | - Elizabeth E. Palmer
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Sydney Children's Hospital, Randwick, NSW, Australia
- School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
- Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David Veivers
- ENT Department, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Marcel E. Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Hospital Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Alan Mackay-Sim
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Mark J. Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Hospital Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn M. Sue
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital, St. Leonards, NSW, Australia
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