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Dyke J, Calapre L, Beasley A, Gray E, Allcock R, Bentel J. Application of multiplex ligation-dependent probe amplification (MLPA) and low pass whole genome sequencing (LP-WGS) to the classification / characterisation of low grade glioneuronal tumours. Pathol Res Pract 2022; 229:153724. [DOI: 10.1016/j.prp.2021.153724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
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Edwards S, Ong R, Davis M, Allcock R, Androga G, Kamien B, Harrop K, Ravenscroft G, Fietz M, Pachter N, Beilby J, Laing N. HIGHLIGHTS ACROSS MYOLOGY. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Haslam S, Salazar L, Allcock R. Genetic testing for familial hypercholesterolaemia, are we testing the right patients? ATHEROSCLEROSIS SUPP 2019. [DOI: 10.1016/j.atherosclerosissup.2019.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Beasley A, Isaacs T, Khattak MA, Freeman JB, Allcock R, Chen FK, Pereira MR, Yau K, Bentel J, Vermeulen T, Calapre L, Millward M, Ziman MR, Gray ES. Clinical Application of Circulating Tumor Cells and Circulating Tumor DNA in Uveal Melanoma. JCO Precis Oncol 2018; 2:1700279. [PMID: 32913999 PMCID: PMC7446501 DOI: 10.1200/po.17.00279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To evaluate the feasibility of using circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) for the management of uveal melanoma (UM). Patients and Methods Low-coverage whole-genome sequencing was used to determine somatic chromosomal copy number alterations (SCNAs) in primary UM tumors, ctDNA, and whole-genome amplified CTCs. CTCs were immunocaptured using an antimelanoma-associated chondroitin sulfate antibody conjugated to magnetic beads and immunostained for melanoma antigen recognised by T cells 1 (MART1)/glycoprotein 100 (gp100)/S100 calcium-binding protein β (S100β). ctDNA was quantified using droplet digital polymerase chain reaction assay for mutations in the GNAQ, GNA11, PLCβ4, and CYSLTR2 genes. Results SCNA analysis of CTCs and ctDNA isolated from a patient with metastatic UM showed good concordance with the enucleated primary tumor. In a cohort of 30 patients with primary UM, CTCs were detected in 58% of patients (one to 37 CTCs per 8 mL of blood), whereas only 26% of patients had detectable ctDNA (1.6 to 29 copies/mL). The presence of CTCs or ctDNA was not associated with tumor size or other prognostic markers. However, the frequent detection of CTCs in patients with early-stage UM supports a model in which CTCs can be used to derive tumor-specific SCNA relevant for prognosis. Monitoring of ctDNA after treatment of the primary tumor allowed detection of metastatic disease earlier than 18F-labeled fluorodeoxyglucose positron emission tomography in two patients. Conclusion The presence of CTCs in localized UM can be used to ascertain prognostic SCNA, whereas ctDNA can be used to monitor patients for early signs of metastatic disease. This study paves the way for the analysis of CTCs and ctDNA as a liquid biopsy that will assist with treatment decisions in patients with UM.
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Affiliation(s)
- Aaron Beasley
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Timothy Isaacs
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Muhammad A Khattak
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - James B Freeman
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Richard Allcock
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Fred K Chen
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Michelle R Pereira
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Kyle Yau
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Jaqueline Bentel
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Tersia Vermeulen
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Leslie Calapre
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Michael Millward
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Melanie R Ziman
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Elin S Gray
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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Bentel JM, Thomas MA, Rodgers JJ, Arooj M, Gray E, Allcock R, Fermoyle S, Mancera RL, Cannell P, Parry J. Erdheim-Chester disease associated with a novel, complex BRAF p.Thr599_Val600delinsArgGlu mutation. BMJ Case Rep 2017; 2017:bcr-2017-219720. [PMID: 28455460 DOI: 10.1136/bcr-2017-219720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BRAF mutation testing to determine eligibility for treatment with vemurafenib was performed on archival skin lesions of a 54-year-old patient diagnosed with Erdheim-Chester disease (ECD) in 1999. Sanger sequencing of DNA extracted from a 2008 skin lesion identified two non-contiguous base substitutions in BRAF, which were shown by next-generation sequencing (NGS) to be located in the same allele. Due to its long-standing duration, molecular evolution of disease was possible; however, both Sanger and NGS of a 2000 skin lesion were unsuccessful due to the poor quality of DNA. Finally, droplet digital PCR using a probe specific for this novel mutation detected the complex BRAF mutation in both the 2000 and 2008 lesions, indicating this case to be ECD with a novel underlying BRAF p.Thr599_Val600delinsArgGlu mutation. Although well at present, molecular modelling of the mutant BRAF suggests suboptimal binding of vemurafenib and hence reduced therapeutic effectiveness.
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Affiliation(s)
- Jacqueline May Bentel
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Australia.,Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Australia
| | - Marc Andrew Thomas
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Australia.,PathWest Molecular Anatomical Pathology, QEII Medical Centre, Nedlands, Australia
| | - Jamie John Rodgers
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Australia
| | - Mahreen Arooj
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia
| | - Elin Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Richard Allcock
- Translational Cancer Pathology Laboratory, Pathwest Laboratory Medicine, QEII Medical Centre, Nedlands, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Soraya Fermoyle
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Australia
| | - Ricardo Luis Mancera
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia
| | - Paul Cannell
- Haematology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Australia
| | - Jeremy Parry
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Australia
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Nguyen LT, Burnett JR, Bell DA, Watts GF, Bates TR, Pang J, Allcock R, Hooper AJ. Improved detection of genetic hypercholesterolaemia using a custom cardiometabolic gene panel. Pathology 2017. [DOI: 10.1016/j.pathol.2016.12.276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Huang B, Firth C, Watterson D, Allcock R, Colmant AMG, Hobson-Peters J, Kirkland P, Hewitson G, McMahon J, Hall-Mendelin S, van den Hurk AF, Warrilow D. Genetic Characterization of Archived Bunyaviruses and their Potential for Emergence in Australia. Emerg Infect Dis 2016; 22:833-40. [PMID: 27088588 PMCID: PMC4861517 DOI: 10.3201/eid2205.151566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Genetic relationships between bunyaviruses from Australia and pathogenic bunyaviruses from elsewhere indicate emergence potential. To better understand the diversity of bunyaviruses and their circulation in Australia, we sequenced 5 viruses (Gan Gan, Trubanaman, Kowanyama, Yacaaba, and Taggert) isolated and serologically identified 4 decades ago as members of the family Bunyaviridae. Gan Gan and Trubanaman viruses almost perfectly matched 2 recently isolated, purportedly novel viruses, Salt Ash and Murrumbidgee viruses, respectively. Kowanyama and Yacaaba viruses were identified as being related to members of a large clade containing pathogenic viruses. Taggert virus was confirmed as being a nairovirus; several viruses of this genus are pathogenic to humans. The genetic relationships and historical experimental infections in mice reveal the potential for these viruses to lead to disease emergence.
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Davis M, Allcock R, Laing N. Next generation sequencing for neuromuscular disease in a diagnostic setting – The Perth custom neuromuscular gene panel 3 years on. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Hobson-Peters J, Warrilow D, McLean BJ, Watterson D, Colmant AMG, van den Hurk AF, Hall-Mendelin S, Hastie ML, Gorman JJ, Harrison JJ, Prow NA, Barnard RT, Allcock R, Johansen CA, Hall RA. Discovery and characterisation of a new insect-specific bunyavirus from Culex mosquitoes captured in northern Australia. Virology 2016; 489:269-81. [PMID: 26773387 DOI: 10.1016/j.virol.2015.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 09/21/2015] [Accepted: 11/05/2015] [Indexed: 11/25/2022]
Abstract
Insect-specific viruses belonging to significant arboviral families have recently been discovered. These viruses appear to be maintained within the insect population without the requirement for replication in a vertebrate host. Mosquitoes collected from Badu Island in the Torres Strait in 2003 were analysed for insect-specific viruses. A novel bunyavirus was isolated in high prevalence from Culex spp. The new virus, provisionally called Badu virus (BADUV), replicated in mosquito cells of both Culex and Aedes origin, but failed to replicate in vertebrate cells. Genomic sequencing revealed that the virus was distinct from sequenced bunyavirus isolates reported to date, but phylogenetically clustered most closely with recently discovered mosquito-borne, insect-specific bunyaviruses in the newly proposed Goukovirus genus. The detection of a functional furin cleavage motif upstream of the two glycoproteins in the M segment-encoded polyprotein suggests that BADUV may employ a unique strategy to process the virion glycoproteins.
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Affiliation(s)
- Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia.
| | - David Warrilow
- Public Health Virology Forensic and Scientific Services, Department of Health, Queensland Government, PO Box 594, Archerfield, Queensland 4108, Australia
| | - Breeanna J McLean
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Agathe M G Colmant
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Andrew F van den Hurk
- Public Health Virology Forensic and Scientific Services, Department of Health, Queensland Government, PO Box 594, Archerfield, Queensland 4108, Australia
| | - Sonja Hall-Mendelin
- Public Health Virology Forensic and Scientific Services, Department of Health, Queensland Government, PO Box 594, Archerfield, Queensland 4108, Australia
| | - Marcus L Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia
| | - Jessica J Harrison
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Natalie A Prow
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Ross T Barnard
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Richard Allcock
- Lottery West State Biomedical Facility - Genomics, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Clinical Immunology, Pathwest Laboratory Medicine Western Australia, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Cheryl A Johansen
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Queensland, Australia.
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Beecroft S, Ong R, Yau K, Duff R, Allcock R, Davis M, Lamont P, Laing N. Efficacy of next-generation sequencing in molecular diagnosis of archived DNA samples. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Moses E, Melton P, Johnson M, Gokhale-Agashe D, Rea A, Allcock R, Blangero J, Brennecke S. O4. Genome wide sequencing approaches to identify missing heritability of preeclampsia. Pregnancy Hypertens 2015. [DOI: 10.1016/j.preghy.2015.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Baynam G, Overkov A, Davis M, Mina K, Schofield L, Allcock R, Laing N, Cook M, Dawkins H, Goldblatt J. A germline MTOR mutation in Aboriginal Australian siblings with intellectual disability, dysmorphism, macrocephaly, and small thoraces. Am J Med Genet A 2015; 167:1659-67. [PMID: 25851998 DOI: 10.1002/ajmg.a.37070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 03/06/2015] [Indexed: 11/07/2022]
Abstract
We report on three Aboriginal Australian siblings with a unique phenotype which overlaps with known megalencephaly syndromes and RASopathies, including Costello syndrome. A gain-of-function mutation in MTOR was identified and represents the first reported human condition due to a germline, familial MTOR mutation. We describe the findings in this family to highlight that (i) the path to determination of pathogenicity was confounded by the lack of genomic reference data for Australian Aboriginals and that (ii) the disease biology, functional analyses in this family, and studies on the tuberous sclerosis complex support consideration of an mTOR inhibitor as a therapeutic agent.
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Affiliation(s)
- Gareth Baynam
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Office of Population Health Genomics, Department of Health, Public Health and Clinical Services Division, Government of Western Australia, Perth, Western Australia, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia.,Telethon Kids Institute, Perth, Western Australia, Australia
| | - Angela Overkov
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | - Mark Davis
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Western Australia, Australia
| | - Kym Mina
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Western Australia, Australia
| | - Lyn Schofield
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Richard Allcock
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Western Australia, Australia
| | - Nigel Laing
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Matthew Cook
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,Australia and Translational Research Unit, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Hugh Dawkins
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, Australia.,Centre for Population Health Research, Curtin Health Innovation Research Institute, Curtin University of Technology, Perth, Western Australia, Australia
| | - Jack Goldblatt
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Office of Population Health Genomics, Department of Health, Public Health and Clinical Services Division, Government of Western Australia, Perth, Western Australia, Australia
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Poo YS, Rudd PA, Gardner J, Wilson JAC, Larcher T, Colle MA, Le TT, Nakaya HI, Warrilow D, Allcock R, Bielefeldt-Ohmann H, Schroder WA, Khromykh AA, Lopez JA, Suhrbier A. Multiple immune factors are involved in controlling acute and chronic chikungunya virus infection. PLoS Negl Trop Dis 2014; 8:e3354. [PMID: 25474568 PMCID: PMC4256279 DOI: 10.1371/journal.pntd.0003354] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022] Open
Abstract
The recent epidemic of the arthritogenic alphavirus, chikungunya virus (CHIKV) has prompted a quest to understand the correlates of protection against virus and disease in order to inform development of new interventions. Herein we highlight the propensity of CHIKV infections to persist long term, both as persistent, steady-state, viraemias in multiple B cell deficient mouse strains, and as persistent RNA (including negative-strand RNA) in wild-type mice. The knockout mouse studies provided evidence for a role for T cells (but not NK cells) in viraemia suppression, and confirmed the role of T cells in arthritis promotion, with vaccine-induced T cells also shown to be arthritogenic in the absence of antibody responses. However, MHC class II-restricted T cells were not required for production of anti-viral IgG2c responses post CHIKV infection. The anti-viral cytokines, TNF and IFNγ, were persistently elevated in persistently infected B and T cell deficient mice, with adoptive transfer of anti-CHIKV antibodies unable to clear permanently the viraemia from these, or B cell deficient, mice. The NOD background increased viraemia and promoted arthritis, with B, T and NK deficient NOD mice showing high-levels of persistent viraemia and ultimately succumbing to encephalitic disease. In wild-type mice persistent CHIKV RNA and negative strand RNA (detected for up to 100 days post infection) was associated with persistence of cellular infiltrates, CHIKV antigen and stimulation of IFNα/β and T cell responses. These studies highlight that, secondary to antibodies, several factors are involved in virus control, and suggest that chronic arthritic disease is a consequence of persistent, replicating and transcriptionally active CHIKV RNA. The largest epidemic ever recorded for chikungunya virus (CHIKV) started in 2004 in Africa, then spread across Asia and recently caused tens of thousands of cases in Papua New Guinea and the Caribbean. This mosquito-borne alphavirus primarily causes an often debilitating, acute and chronic polyarthritis/polyarthalgia. Despite robust anti-viral immune responses CHIKV is able to persist, with such persistence poorly understood and the likely cause of chronic disease. Herein we highlight the propensity of CHIKV to persist long term, both as a persistent viraemia in different B cell deficient mouse strains, but also as persistent viral RNA in wild-type mice. These studies suggest that, aside from antibodies, other immune factors, such as CD4 T cells and TNF, are active in viraemia control. The work also supports the notion that CHIKV disease, with the exception of encephalitis, is largely an immunopathology. Persistent CHIKV RNA in wild-type mice continues to stimulate type I interferon and T cell responses, with this model of chronic disease recapitulating many of the features seen in chronic CHIKV patients.
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Affiliation(s)
- Yee Suan Poo
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
- School of Medicine/School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Penny A. Rudd
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
- School of Medicine/School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Joy Gardner
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
| | - Jane A. C. Wilson
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
- School of Medicine/School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Thibaut Larcher
- Institut National de Recherche Agronomique, Unité Mixte de Recherche 703, Oniris, Nantes, France
| | - Marie-Anne Colle
- Institut National de Recherche Agronomique, Unité Mixte de Recherche 703, Oniris, Nantes, France
| | - Thuy T. Le
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
| | - Helder I. Nakaya
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - David Warrilow
- Public Health Virology Laboratory, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Richard Allcock
- Lotterywest State Biomedical Facility Genomics, Royal Perth Hospital, Perth, Western Australia, Australia
| | | | - Wayne A. Schroder
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
| | - Alexander A. Khromykh
- School of Medicine/School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - José A. Lopez
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
- School of Natural Sciences, Griffith University, Nathan, Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, and the Australian Infectious Diseases Research Centre, Brisbane, Queensland, Australia
- School of Medicine/School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland, Australia
- School of Natural Sciences, Griffith University, Nathan, Australia
- * E-mail:
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Masoli M, Menzies-Gow A, Dobson L, Morjaria J, Allcock R, Niven R. S93 A Prospective Study Investigating Exacerbations, Healthcare Utilisation And Health Economic Indicators In Omalizumab Treated Severe Allergic Asthma Patients - Results From An Interim Analysis Of The Apex Ii Study. Thorax 2014. [DOI: 10.1136/thoraxjnl-2014-206260.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Yau K, Allcock R, Mina K, Ravenscroft G, Cabrera M, Gooding R, Wise C, Sivadorai P, Trajanoski D, Atkinson V, Wagner S, Nowak K, Duff R, Lamont P, Davis M, Laing N. G.P.18. Neuromuscul Disord 2014. [DOI: 10.1016/j.nmd.2014.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Barnett CP, Todd EJ, Ong R, Davis MR, Atkinson V, Allcock R, Laing N, Ravenscroft G. Distal arthrogryposis type 5D with novel clinical features and compound heterozygous mutations in ECEL1. Am J Med Genet A 2014; 164A:1846-9. [PMID: 24782201 DOI: 10.1002/ajmg.a.36342] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/06/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Christopher P Barnett
- Pediatric & Reproductive Genetics, SA Clinical Genetics Service, Women's and Children's Hospital/SA Pathology, North Adelaide, South Australia, Australia
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Warrilow D, Watterson D, Hall RA, Davis SS, Weir R, Kurucz N, Whelan P, Allcock R, Hall-Mendelin S, O'Brien CA, Hobson-Peters J. A new species of mesonivirus from the Northern Territory, Australia. PLoS One 2014; 9:e91103. [PMID: 24670468 PMCID: PMC3966781 DOI: 10.1371/journal.pone.0091103] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
Here we describe Casuarina virus (CASV), a new virus in the family Mesoniviridae. This is the first report of a mesonivirus in Australia, which extends the geographical range of this virus family to 3 continents. The virus was isolated in 2010 from Coquillettidia xanthogaster mosquitoes during surveillance in the suburbs of Darwin, the capital of the Northern Territory. Cryo-electron microscopy of the CASV virions revealed spherical particles of 65 nm in size with large club-shaped projections of approximately 15 nm in length. The new virus was most closely related to Alphamesonivirus 1, the only currently recognized species in the family. In 2013 a further 5 putative new mesonivirus species were described: Hana, Méno, Nsé, Moumo and Dak Nong viruses. The evolutionary distance between CASV and two of its closest relatives, Cavally and Hana viruses (Jones-Taylor-Thornton distance of 0.151 and 0.224, respectively), along with its isolation from a different genus of mosquitoes captured on a separate continent indicate that CASV is a new species.
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Affiliation(s)
- David Warrilow
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Archerfield, Queensland, Australia
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Steven S Davis
- Berrimah Veterinary Labs, Department of Primary Industries and Fisheries, Darwin, Northern Territory, Australia
| | - Richard Weir
- Berrimah Veterinary Labs, Department of Primary Industries and Fisheries, Darwin, Northern Territory, Australia
| | - Nina Kurucz
- Centre for Disease Control, Health Protection Division, Northern Territory Department of Health, Darwin, Northern Territory, Australia
| | - Peter Whelan
- Centre for Disease Control, Health Protection Division, Northern Territory Department of Health, Darwin, Northern Territory, Australia
| | - Richard Allcock
- LotteryWest State Biomedical Facility, Genomics, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia; Department of Clinical Immunology, Pathwest Laboratory Medicine Western Australia, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Sonja Hall-Mendelin
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Archerfield, Queensland, Australia
| | - Caitlin A O'Brien
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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Hall-Mendelin S, Allcock R, Kresoje N, van den Hurk AF, Warrilow D. Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing. PLoS One 2013; 8:e58026. [PMID: 23460918 PMCID: PMC3584025 DOI: 10.1371/journal.pone.0058026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
Human disease incidence attributed to arbovirus infection is increasing throughout the world, with effective control interventions limited by issues of sustainability, insecticide resistance and the lack of effective vaccines. Several promising control strategies are currently under development, such as the release of mosquitoes trans-infected with virus-blocking Wolbachia bacteria. Implementation of any control program is dependent on effective virus surveillance and a thorough understanding of virus-vector interactions. Massively parallel sequencing has enormous potential for providing comprehensive genomic information that can be used to assess many aspects of arbovirus ecology, as well as to evaluate novel control strategies. To demonstrate proof-of-principle, we analyzed Aedes aegypti or Aedes albopictus experimentally infected with dengue, yellow fever or chikungunya viruses. Random amplification was used to prepare sufficient template for sequencing on the Personal Genome Machine. Viral sequences were present in all infected mosquitoes. In addition, in most cases, we were also able to identify the mosquito species and mosquito micro-organisms, including the bacterial endosymbiont Wolbachia. Importantly, naturally occurring Wolbachia strains could be differentiated from strains that had been trans-infected into the mosquito. The method allowed us to assemble near full-length viral genomes and detect other micro-organisms without prior sequence knowledge, in a single reaction. This is a step toward the application of massively parallel sequencing as an arbovirus surveillance tool. It has the potential to provide insight into virus transmission dynamics, and has applicability to the post-release monitoring of Wolbachia in mosquito populations.
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Affiliation(s)
- Sonja Hall-Mendelin
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Richard Allcock
- LotteryWest State Biomedical Facility – Genomics, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia
- Department of Clinical Immunology, Pathwest Laboratory Medicine WA, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Nina Kresoje
- LotteryWest State Biomedical Facility – Genomics, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Andrew F. van den Hurk
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
- * E-mail:
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Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 2012; 91:80-8. [PMID: 22849830 DOI: 10.1016/j.mimet.2012.07.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 02/07/2023]
Abstract
Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within different sized semi-conductor chips. Further development of Golay barcoded Ion Tags allowed multiplex analyses of microbial communities with substantially reduced costs compared with platforms such as 454/GS-FLX. Using these protocols we assessed the bacterial and archaeal dynamics within covered anaerobic digesters used to treat piggery wastes. Analysis of these sequence data showed that these novel methanogenic waste treatment systems are dominated by bacterial taxa, in particular Clostridium, Synergistia and Bacteroides that were maintained as a stable community over extended time periods. Archaeal community dynamics were more stochastic with the key methanogenic taxa more difficult to resolve, principally due to the poor congruence seen between community structures generated either by nested PCR or metagenomic approaches for archaeal analyses. Our results show that for microbial community structure and function analyses, the PGM platform provides a low cost, scalable and high throughput solution for both Tag sequencing and metagenomic analyses.
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Affiliation(s)
- Andrew S Whiteley
- Centre for Ecology and Hydrology, Wallingford, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, United Kingdom.
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Crackett R, Day M, DeSoyza J, Lordan J, Fisher A, MacGowan G, Allcock R, Parry G, Corris P. 501 Ten Year Survival in Incident Cases of Idiopathic Pulmonary Arterial Hypertension (IPAH) in the Modern Era. J Heart Lung Transplant 2011. [DOI: 10.1016/j.healun.2011.01.512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Mastaglia FL, Needham M, Scott A, James I, Zilko P, Day T, Kiers L, Corbett A, Witt CS, Allcock R, Laing N, Garlepp M, Christiansen FT. Sporadic inclusion body myositis: HLA-DRB1 allele interactions influence disease risk and clinical phenotype. Neuromuscul Disord 2009; 19:763-5. [DOI: 10.1016/j.nmd.2009.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 07/29/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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Smallwood L, Warrington N, Allcock R, van Bockxmeer F, Palmer L, Iacopetta B, Golledge J, Norman P. Matrix Metalloproteinase-2 Gene Variants and Abdominal Aortic Aneurysm. Eur J Vasc Endovasc Surg 2009; 38:169-71. [DOI: 10.1016/j.ejvs.2009.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 04/24/2009] [Indexed: 11/25/2022]
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24
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Valente FP, Tan C, Phipps M, Witt CS, Kaur G, Gut I, Allcock R, Price P. TNF block haplotypes associated with conserved MHC haplotypes in European, Asian and Australian Aboriginal donors. ACTA ACUST UNITED AC 2009; 74:57-61. [DOI: 10.1111/j.1399-0039.2009.01258.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Almeida OP, Norman PE, Allcock R, van Bockxmeer F, Hankey GJ, Jamrozik K, Flicker L. Polymorphisms of the CRP gene inhibit inflammatory response and increase susceptibility to depression: the Health in Men Study. Int J Epidemiol 2009; 38:1049-59. [PMID: 19433520 DOI: 10.1093/ije/dyp199] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Depression has been associated with chronic changes in the serum concentration of C-reactive protein (CRP) in observational studies, but it is unclear if this association is causal or is due to confounding and bias. Genetic studies are less subject to this type of error and offer an opportunity to investigate if CRP is causally linked to depression, particularly because known polymorphisms of the CRP gene have been associated with high- and low-basal serum concentrations of CRP [single nucleotide polymorphisms (SNPs) rs1130864 and rs1205, respectively]. The aim of this study is to determine if polymorphisms of SNPs rs1130864 and rs1205 are associated with prevalent depression. METHODS We completed a cross-sectional study of a community sample of 3700 men aged > or = 70 years, and used the 15-item Geriatric Depression Scale (GDS-15) to assess depressive symptoms. A GDS-15 score 7 or more indicates the presence of clinically significant depressive symptoms. Physical morbidity was assessed with the physical component summary score (PCS) of the SF-36 Health Survey. We collected fasting blood samples to measure high sensitivity CRP and to extract DNA for the genotyping of SNPs rs1130864 and rs1205 of the CRP gene. RESULTS One hundred and eighty-two men were depressed (4.9%). The odds of depression increased by 2% (95% CI = 1-4%) for every unit (mg/l) increase of CRP and nearly doubled for men with CRP > or = 3 mg/l vs <1 mg/l [odds ratio (OR) = 1.95, 95% confidence interval (CI) = 1.27-2.98]. However, the association between high CRP (> or = 3 mg/l) and depression was no longer significant after the analyses were adjusted for smoking, age, body mass index (BMI) and PCS. Men with the CT and TT genotypes of rs1130864 had 1.36 (95% CI = 1.13-1.63) and 2.31 (95% CI = 1.65-3.24) greater odds of CRP > or = 3 mg/l than CC carriers, but there was no association between this polymorphism and the presence of prevalent depression. The G > A polymorphism of SNP rs1205 was associated with 24% (95% CI = 16-32%) lower concentration of CRP compared with other genotypes. Men with the rs1205 AA genotype had 1.66 (95% CI = 1.07-2.57) and 1.67 (95% CI = 1.08-2.58) greater odds of having clinically significant depression than participants with the GA and GG genotypes, respectively. CONCLUSION Our study shows that clinically significant depressive symptoms in later life are unlikely to be caused by an increase in the serum concentration of CRP. Instead, we found that the risk of depression was greater amongst people who carry the rs1205 G > A genetic polymorphism of the CRP gene, which was associated with approximately 20% lower serum concentration of CRP compared with other genotypes. This suggests that CRP may be a compensatory response to external insults that predispose to depression, and that an increase in the concentration of CRP might be adaptive.
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Affiliation(s)
- Osvaldo P Almeida
- Western Australian Centre for Health & Ageing, Perth, WA, Australia.
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Needham M, Scott A, Christiansen F, James I, Corbett A, Day T, Kiers L, Laing N, Allcock R, Mastaglia F. G.P.5.06 HLA alleles and MHC haplotypes in sporadic inclusion body myositis: Frequencies and phenotypic correlations. Neuromuscul Disord 2008. [DOI: 10.1016/j.nmd.2008.06.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Smallwood L, Allcock R, van Bockxmeer F, Warrington N, Palmer LJ, Iacopetta B, Golledge J, Norman PE. Polymorphisms of the matrix metalloproteinase 9 gene and abdominal aortic aneurysm. Br J Surg 2008; 95:1239-44. [PMID: 18763261 DOI: 10.1002/bjs.6345] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Increased matrix metalloproteinase (MMP) 9 activity has been implicated in the formation of abdominal aortic aneurysm (AAA). The aim was to explore the association between potentially functional variants of the MMP-9 gene and AAA. METHODS The -1562C > T and -1811A > T variants of the MMP-9 gene were genotyped in 678 men with an AAA (at least 30 mm in diameter) and 659 control subjects (aortic diameter 19-22 mm) recruited from a population-based trial of screening for AAA. Levels of MMP-9 were measured in a random subset of 300 cases and 84 controls. The association between genetic variants (including haplotypes) and AAA was assessed by multivariable logistic regression. RESULTS There was no association between the MMP-9-1562C > T (odds ratio (OR) 0.70 (95 per cent confidence interval (c.i.) 0.27 to 1.82)) or -1811A > T (OR 0.71 (95 per cent c.i. 0.28 to 1.85)) genotypes, or the most common haplotype (OR 0.81 (95 per cent c.i. 0.62 to 1.05)) and AAA. The serum MMP-9 concentration was higher in cases than controls, and in minor allele carriers in cases and controls, although the differences were not statistically significant. CONCLUSION In this study, the genetic tendency to higher levels of circulating MMP-9 was not associated with AAA.
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Affiliation(s)
- L Smallwood
- Schools of Surgery, University of Western Australia, Fremantle, Western Australia
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Shipley M, Allcock R. Achieving a smoke-free hospital: reported enforcement of smoke-free regulations by NHS health care staff. J Public Health (Oxf) 2008; 30:2-7. [DOI: 10.1093/pubmed/fdn004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Smallwood L, Allcock R, van Bockxmeer F, Warrington N, Palmer LJ, Iacopetta B, Norman PE. Polymorphisms of the interleukin-6 gene promoter and abdominal aortic aneurysm. Eur J Vasc Endovasc Surg 2007; 35:31-6. [PMID: 17996468 DOI: 10.1016/j.ejvs.2007.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 08/30/2007] [Indexed: 11/17/2022]
Abstract
BACKGROUND Elevated levels of circulating interleukin-6 (IL-6) have been reported in patients with abdominal aortic aneurysms (AAAs). Although this implicates inflammation as a cause of AAAs, there is also evidence that the aneurysmal aorta may secrete IL-6 into the circulation as a result of aortic proteolysis. Genetic association studies are one means of trying to clarify the role of specific mediators in the causal pathway. The aim of the present study was to examine the association between variants of the IL-6 gene and AAAs. METHODS An association study involving 677 men with screen-detected AAAs and 656 age-matched controls was performed. Three variants in the IL-6 promoter region were analysed: IL-6-174G>C (rs1800795), IL-6-572G>C (rs1800796) and IL-6-597G>A (rs1800797). Univariate regression of SNP genotype on AAA as a binary outcome was initially performed under a range of genetic models (additive, dominant and recessive). This was followed by multivariate analyses, testing the same models but including risk factors known to be associated with AAAs. All analyses and haplotype estimation were performed under a generalized linear model framework. RESULTS IL-6-572G>C polymorphism (frequency 1.5% in cases) was identified as an independent risk factor for AAA with an odds ratio (OR) of 6.00 (95%CI: 1.22, 29.41) when applied to the recessive model. No association was seen in the additive or dominant models. In a multivariate analysis using the most common haplotype (h.111, frequency 48.7%) as a reference, h.211 (frequency 4.4%) was an independent risk factor for AAA (OR 1.56, 95%CI: 1.02, 2.39). CONCLUSION The IL-6 572G>C polymorphism (and h.211 haplotype) is associated with AAA, however it is too rare to be an important cause of most AAAs. This does not support the concept that the elevated level of IL-6 reported in patients with AAAs is a primary cause of the aneurysmal process.
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Affiliation(s)
- L Smallwood
- School of Surgery and Pathology, University of Western Australia
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Allcock R, Dolecki KJ, Boodhoo A, Abdul Khalil A, Wong AML, Price P. Genomic sequence and expression profile of murine Bat1a and Nfkbil1. ACTA ACUST UNITED AC 2007; 17:292-9. [PMID: 17312949 DOI: 10.1080/10425170600885807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In humans, susceptibility to several immunopathologic diseases maps to a conserved block encompassing the polymorphic BAT1, NFKBIL1 (IKBL) and TNF genes in the central MHC. As a pre-requisite for studies of these genes in animal models, we characterized Bat1a and Nfkbil1 in inbred mice differing in their H2 haplotype. We identified two indels and nine single nucleotide polymorphisms (SNP) upstream of Nfkbil1, one indel, nine SNP upstream of Bat1a and a synonymous SNP in exon 2 of Bat1a. H2(g7) and H2(b) mice yielded identical Bat1a and Nfkbil1 sequences. Real time PCR (RT-PCR) showed Bat1a was expressed in adult brain, heart, kidney, liver, lung, pancreas and spleen. Expression of Bat1a was higher in brain and liver of 15-day embryos compared to 1-day old mice and increased moderately in liver and lung of adult mice 2-4 h after LPS challenge. Nfkbil1 expression was low or undetetectable in all tissues and cell lines.
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Affiliation(s)
- Richard Allcock
- School of Surgery and Pathology, University of Western Australia, Nedlands 6009, WA, Australia
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Windsor L, Puschendorf M, Allcock R, Scott A, Sayer D, Kucharzak R, Gut I, McCann V, Davis E, Witt C, Christiansen F, Price P. Does a central MHC gene in linkage disequilibrium with HLA-DRB1*0401 affect susceptibility to type 1 diabetes? Genes Immun 2005; 6:298-304. [PMID: 15858601 DOI: 10.1038/sj.gene.6364210] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Subtypes of HLA-DR4 are associated with susceptibility or protection against type 1 diabetes (T1DM). We addressed whether this reflects linkage disequilibrium with the true susceptibility locus by studying broader MHC haplotypes marked by alleles of HLA-B, IKBL (adjacent to TNFA) and complement C4. The study used a largely Caucasian cohort from Western Australia. HLA-DRB1*0401 and HLA-DRB1*0405 marked susceptibility to T1DM. In Caucasians, DRB1*0401 occurs predominantly in the 44.1 ancestral haplotype (AH; HLA-A2,B44, DRB1*0401,DQB1*0301) and the 62.1AH (HLA-A2,B15(62),DRB1*0401,DQB1*0302). HLA-B15 marked susceptibility and HLA-B44 marked with resistance to T1DM in patients and controls preselected for HLA-DRB1*0401. A gene between TNFA and HLA-B on the 8.1AH (HLA-A1,B8,;DR3,DQ2) modifies the effects of the class II alleles. Here, alleles characteristic of the 62.1AH (C4B3, IKBL+446*T and HLA-A2,B15) were screened in donors preselected for HLA-DRB1*0401. C4B3 was associated with diabetes, consistent with a diabetes gene telomeric of MHC class II. However, increases in carriage of IKBL+446*T and HLA-A2,B15 were marginal, as too few control subjects were available with the diabetogenic alleles. However, with these tools, selection of HLA-DRB1*0401, DQB1*0302 donors who are positive and negative for C4B3 will allow bidirectional mapping of diabetes genes in the central MHC.
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Affiliation(s)
- L Windsor
- Department of Clinical Immunology and Biochemical Genetics, Royal Perth Hospital, Perth, Australia
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Price P, Santoso L, Mastaglia F, Garlepp M, Kok CC, Allcock R, Laing N. Two major histocompatibility complex haplotypes influence susceptibility to sporadic inclusion body myositis: critical evaluation of an association with HLA-DR3. ACTA ACUST UNITED AC 2005; 64:575-80. [PMID: 15496200 DOI: 10.1111/j.1399-0039.2004.00310.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies of sporadic inclusion body myositis (sIBM) have shown a strong association with HLA-DR3 and other components of the 8.1 ancestral haplotype (AH) (HLA-A1, B8, DR3), where the susceptibility locus has been mapped to the central major histocompatibility complex (MHC) region between HLA-DR and C4. Here, the association with HLA-DR3 and other genes in the central MHC and class II region was further investigated in a group of 42 sIBM patients and in an ethnically similar control group (n = 214), using single-nucleotide polymorphisms and microsatellite screening. HLA-DR3 (marking DRB1*0301 in Caucasians) was associated with sIBM (Fisher's test). However, among HLA-DR3-positive patients and controls, carriage of HLA-DR3 without microsatellite and single-nucleotide polymorphism alleles of the 8.1AH (HLA-A1, B8, DRB3*0101, DRB1*0301, DQB1*0201) was marginally less common in patients. Patients showed no increase in carriage of the 18.2AH (HLA-A30, B18, DRB3*0202, DRB1*0301, DQB1*0201) or HLA-DR3 without the central MHC of the 8.1AH, further arguing against HLA-DRB1 as the direct cause of susceptibility. Genes between HLA-DRB1 and HOX12 require further investigation. BTL-II lies in this region and is expressed in muscle. Carriage of allele 2 (exon 6) was more common in patients. BTL-II(E6)*2 is characteristic of the 35.2AH (HLA-A3, B35, DRB1*01) in Caucasians and HLA-DR1, BTL-II(E6)*2, HOX12*2, RAGE*2 was carried by several patients. The 8.1AH and 35.2AH may confer susceptibility to sIBM independently or share a critical allele.
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Affiliation(s)
- P Price
- School of Surgery and Pathology, University of Western Australia, Nedlands, Australia.
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Allcock R, Cheong K, Christiansen F, Witt C. Comment to: Gambelunghe G., Ghaderi, Cosentino A et al. (2000) association of MHC class I chain-related A (MIC-A) gene polymorphism with type I diabetes. Diabetologia 43: 507-514. Diabetologia 2001; 44:514-6. [PMID: 11357484 DOI: 10.1007/s001250051651] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Thomson JR, Machado RD, Pauciulo MW, Morgan NV, Humbert M, Elliott GC, Ward K, Yacoub M, Mikhail G, Rogers P, Newman J, Wheeler L, Higenbottam T, Gibbs JS, Egan J, Crozier A, Peacock A, Allcock R, Corris P, Loyd JE, Trembath RC, Nichols WC. Sporadic primary pulmonary hypertension is associated with germline mutations of the gene encoding BMPR-II, a receptor member of the TGF-beta family. J Med Genet 2000; 37:741-5. [PMID: 11015450 PMCID: PMC1757155 DOI: 10.1136/jmg.37.10.741] [Citation(s) in RCA: 466] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Primary pulmonary hypertension (PPH), resulting from occlusion of small pulmonary arteries, is a devastating condition. Mutations of the bone morphogenetic protein receptor type II gene (BMPR2), a component of the transforming growth factor beta (TGF-beta) family which plays a key role in cell growth, have recently been identified as causing familial PPH. We have searched for BMPR2 gene mutations in sporadic PPH patients to determine whether the same genetic defect underlies the more common form of the disorder. METHODS We investigated 50 unrelated patients, with a clinical diagnosis of PPH and no identifiable family history of pulmonary hypertension, by direct sequencing of the entire coding region and intron/exon boundaries of the BMPR2 gene. DNA from available parent pairs (n=5) was used to assess the occurrence of spontaneous (de novo) mutations contributing to sporadic PPH. RESULTS We found a total of 11 different heterozygous germline mutations of the BMPR2 gene in 13 of the 50 PPH patients studied, including missense (n=3), nonsense (n=3), and frameshift (n=5) mutations each predicted to alter the cell signalling response to specific ligands. Parental analysis showed three occurrences of paternal transmission and two of de novo mutation of the BMPR2 gene in sporadic PPH. CONCLUSION The sporadic form of PPH is associated with germline mutations of the gene encoding the receptor protein BMPR-II in at least 26% of cases. A molecular classification of PPH, based upon the presence or absence of BMPR2 mutations, has important implications for patient management and screening of relatives.
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Affiliation(s)
- J R Thomson
- Division of Medical Genetics, Departments of Medicine and Genetics, University of Leicester, UK
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Price P, Witt C, Allcock R, Sayer D, Garlepp M, Kok CC, French M, Mallal S, Christiansen F. The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunopathological diseases. Immunol Rev 1999; 167:257-74. [PMID: 10319267 DOI: 10.1111/j.1600-065x.1999.tb01398.x] [Citation(s) in RCA: 385] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An individual's major histocompatibility complex (MHC) ancestral haplotype (AH) is the clearest single determinant of susceptibility to MHC associated immunopathological disease, as it defines the alleles carried at all loci in the MHC. However, the direct effects of any of the 150-200 genes that constitute the MHC are difficult to determine since recombination only occurs at defined hotspots. This review concerns the 8.1 AH (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2), which is carried by most Caucasians with HLA-B8. It is associated with accelerated human immunodeficiency virus (HIV) disease, and susceptibility to insulin-dependent diabetes mellitus (IDDM), systemic lupus erythematosus, dermatitis herpetiformis, common variable immunodeficiency and IgA deficiency, myasthenia gravis and several other conditions. We have mapped susceptibility genes for HIV, IDDM and myasthenia gravis to the central MHC between HLA-B and the tumour necrosis factor or complement genes. Here we consider which of the remaining 8.1-associated diseases are more closely associated with HLA-DR3 and/or DQ2. Several candidate genes in the central MHC have the potential to modulate immune or inflammatory responses in an antigen-independent manner, as is seen in studies of cultured cells from healthy carriers of the 8.1 AH. Hence these genes may act as a common co-factor in the diverse immunopathological conditions associated with the 8.1 AH.
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Affiliation(s)
- P Price
- Department of Clinical Immunology, Royal Perth Hospital, Western Australia, Australia
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Abstract
In view of the difficulty encountered in distinguishing between 2 degrees renal cell carcinoma (RCC) and hemangioblastoma (HBl) in the central nervous system, the AgNOR technique has been applied empirically to a series of 16 specimens of HBl, 5 primary RCC, and 6 specimens of secondary RCC in the CNS. To avoid tautology, the nature of these was confirmed by immunostaining for epithelial membrane antigen (EMA) and factor VIII-related antigen (FVII RAg). It was found that mean nuclear AgNOR counts in the stromal and endothelial cells of HBl exceeded significantly the counts in the tumor and endothelial cells of RCC, with no overlap in values. It is suggested that the AgNOR method is a useful adjunct in achieving the differential diagnosis of HBl and RCC in the nervous system.
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Affiliation(s)
- J Crocker
- Department of Histopathology, East Birmingham Hospital, United Kingdom
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