ORCID Profile
0000-0003-1940-0007
Current Organisation
University of Tasmania
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Publisher: Springer Science and Business Media LLC
Date: 12-2010
Publisher: AME Publishing Company
Date: 2018
Publisher: MDPI AG
Date: 06-04-2022
DOI: 10.3390/IJMS23074042
Abstract: Intraocular anti-vascular endothelial growth factor (VEGF) therapies are the front-line treatment for diabetic macular edema (DME) however, treatment response varies widely. This study aimed to identify genetic determinants associated with anti-VEGF treatment response in DME. We performed a genome-wide association study on 220 Australian patients with DME treated with anti-VEGF therapy, genotyped on the Illumina Global Screening Array, and imputed to the Haplotype Reference Consortium panel. The primary outcome measures were changes in central macular thickness (CMT in microns) and best-corrected visual acuity (BCVA in ETDRS letters) after 12 months. Association between single nucleotide polymorphism (SNP) genotypes and DME outcomes were evaluated by linear regression, adjusting for the first three principal components, age, baseline CMT/BCVA, duration of diabetic retinopathy, and HbA1c. Two loci reached genome-wide significance (p 5 × 10−8) for association with increased CMT: a single SNP on chromosome 6 near CASC15 (rs78466540, p = 1.16 × 10−9) and a locus on chromosome 12 near RP11-116D17.1 (top SNP rs11614480, p = 2.69 × 10−8). Four loci were significantly associated with reduction in BCVA: two loci on chromosome 11, downstream of NTM (top SNP rs148980760, p = 5.30 × 10−9) and intronic in RP11-744N12.3 (top SNP rs57801753, p = 1.71 × 10−8) one near PGAM1P1 on chromosome 5 (rs187876551, p = 1.52 × 10−8) and one near TBC1D32 on chromosome 6 (rs118074968, p = 4.94 × 10−8). In silico investigations of each locus identified multiple expression quantitative trait loci and potentially relevant candidate genes warranting further analysis. Thus, we identified multiple genetic loci predicting treatment outcomes for anti-VEGF therapies in DME. This work may potentially lead to managing DME using personalized treatment approaches.
Publisher: Hindawi Limited
Date: 12-11-2020
DOI: 10.1155/2020/5016916
Abstract: Diabetic retinopathy (DR) is the most common microvascular complication of diabetes mellitus (DM). DR is complex and the term encompasses several clinical subtypes of diabetic eye disease, including diabetic macular edema (DME), the most frequent cause of central vision loss in DR patients. Both genetic and environmental factors contribute to the pathophysiology of DR and its subtypes. While numerous studies have identified several susceptibility genes for DR, few have investigated the impact of genetics on DME susceptibility. This review will focus on the current literature surrounding genetic risk factors associated with DME. We will also highlight the small number of studies investigating the genetics of response to antivascular endothelial growth factor (anti-VEGF) injection, which is used to treat DME.
Publisher: Springer Science and Business Media LLC
Date: 2010
Publisher: Springer Science and Business Media LLC
Date: 12-2001
Abstract: There is an apparent paradox in our understanding of molecular evolution. Current biochemically based models predict that evolutionary trees should not be recoverable for ergences beyond a few hundred million years. In practice, however, trees often appear to be recovered from much older times. Mathematical models, such as those assuming that sites evolve at different rates [including a Gamma distribution of rates across sites (RAS)] may in theory allow the recovery of some ancient ergences. However, such models require that each site maintain its characteristic rate over the whole evolutionary period. This assumption, however, contradicts the knowledge that tertiary structures erge with time, invalidating the rate-constancy assumption of purely mathematical models. We report here that a hidden Markov version of the covarion model can meet both biochemical and statistical requirements for the analysis of sequence data. The model was proposed on biochemical grounds and can be implemented with only two additional parameters. The two hidden parts of this model are the proportion of sites free to vary (covarions) and the rate of interchange between fixed sites and these variable sites. Simulation results are consistent with this approach, providing a better framework for understanding anciently erged sequences than the standard RAS models. However, a Gamma distribution of rates may approximate a covarion model and may possibly be justified on these grounds. The accurate reconstruction of older ergences from sequence data is still a major problem, and molecular evolution still requires mathematical models that also have a sound biochemical basis.
Publisher: BMJ
Date: 08-2022
DOI: 10.1136/BMJOPHTH-2022-001064
Abstract: Paediatric (childhood or congenital) cataract is an opacification of the normally clear lens of the eye and has a genetic basis in at least 18% of cases in Australia. This study aimed to replicate clinical gene screening to identify variants likely to be causative of disease in an Australian patient cohort. Sixty-three reported isolated cataract genes were screened for rare coding variants in 37 Australian families using genome sequencing. Disease-causing variants were confirmed in eight families with variant classification as ‘likely pathogenic’. This included novel variants PITX3 p.(Ter303LeuextTer100), BFSP1 p.(Glu375GlyfsTer2), and GJA8 p.(Pro189Ser), as well as, previously described variants identified in genes GJA3, GJA8, CRYAA, BFSP1, PITX3, COL4A1 and HSF4 . Additionally, eight variants of uncertain significance with evidence towards pathogenicity were identified in genes: GJA3, GJA8, LEMD2, PRX, CRYBB1, BFSP2, and MIP . These findings expand the genotype–phenotype correlations of both pathogenic and benign variation in cataract-associated genes. They further emphasise the need to develop additional evidence such as functional assays and variant classification criteria specific to paediatric cataract genes to improve interpretation of variants and molecular diagnosis in patients.
Publisher: Oxford University Press (OUP)
Date: 15-10-2015
DOI: 10.1093/GBE/EVV196
Publisher: Informa UK Limited
Date: 08-08-2014
DOI: 10.3109/19401736.2014.947583
Abstract: We present the complete mitochondrial genome (accession number: LK995454) of an iconic Australian species, the eastern grey kangaroo (Macropus giganteus). The mitogenomic organization is consistent with other marsupials, encoding 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, an origin of light strand replication and a control region or D-loop. No repetitive sequences were detected in the control region. The M. giganteus mitogenome exemplifies a combination of tRNA gene order and structural peculiarities that appear to be unique to marsupials. We present a maximum likelihood phylogeny based on complete mitochondrial protein and RNA coding sequences that confirms the phylogenetic position of the grey kangaroo among macropodids.
Publisher: American Medical Association (AMA)
Date: 02-2020
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 20-09-2019
Abstract: Few studies have explored the association of genetic variants in microRNA genes and binding sites with diabetic retinopathy (DR) in type 1 diabetes. We conducted a genome-wide scan for single nucleotide polymorphisms (SNPs) in these genes by using data from a genome-wide association study (GWAS). All known SNPs were imputed from our GWAS data (n = 325) of DR cases and diabetic controls (no DR). Relevant SNPS were extracted using miRNASNP and PolymiRTS (version 2) databases. χ2 tests and logistic regression (adjusting for age, sex, duration of diabetes, HbA1c, and hypertension) were used to test the association between the imputed SNPs and DR phenotypes (any DR, nonproliferative DR [NPDR], proliferative DR [PDR], diabetic macular edema [DME], and sight-threatening DR defined as PDR, severe NPDR, or clinically significant macula edema [CSME]) compared with diabetic controls. Top-ranking SNPs were genotyped in a larger cohort (N = 560) to confirm their association with DR. Three SNPs (rs10061133, rs1049835, rs9501255) were selected and genotyped in the final cohort. Rs10061133 in MIR449b was protective of sight-threatening DR (odds ratio [OR] = 0.32, P = 3.68 × 10-4) and PDR (OR = 0.30, P = 8.12 × 10-4), and the associations became more significant as the cohort increased in size. Rs10061133 in MIR449b is significantly associated with a decreased risk of PDR and sight-threatening DR in Caucasian patients with type 1 diabetes. This can guide future studies on genetic risk profiling and on developing microRNA-related therapies for sight-threatening DR.
Publisher: Oxford University Press (OUP)
Date: 26-05-2010
DOI: 10.1093/GBE/EVQ029
Publisher: Frontiers Media SA
Date: 19-03-2019
Publisher: Cold Spring Harbor Laboratory
Date: 11-03-2020
DOI: 10.1101/2020.03.09.972364
Abstract: Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over two time scales: one based on the Adélie penguin s les dating to approximately 46.5 kya, the other dating to the ersification of chordates more than 500 Mya. We show that the process of microsatellite allele length evolution is at dynamic equilibrium while there is length polymorphism among in iduals, the length distribution for a given locus remains stable. Many microsatellites persist over very long time scales, particularly in exons and regulatory sequence. These often retain length variability, suggesting that they may play a role in the maintenance of evolutionary plasticity.
Publisher: BMJ
Date: 05-2021
DOI: 10.1136/BMJOPHTH-2021-000749
Abstract: To compare the visual outcomes of intravitreal antivascular endothelial growth factor (anti-VEGF) injections in neovascular age-related macular degeneration (nAMD), diabetic macular oedema (DMO) and retinal vein occlusion (RVO) in a real-world setting. Retrospective analysis of data from the Tasmanian Ophthalmic Biobank database. The median change in best-corrected visual acuity (BCVA) between baseline and 12 months post initiating intravitreal anti-VEGF treatment were compared between the three diseases. Final BCVA, central macular thickness (CMT), cumulative number of injections and overall predictors of change in BCVA and CMT were also determined. At 12 months, change in BCVA was significantly different between nAMD, DMO and RVO cohorts (p=0.032), with lower median change for DMO (2 letters, range −5 to 20) than for RVO (11 letters, range −20 to 35). Likewise, CMT change was significantly different between the three cohorts (p=0.022), with a smaller reduction in CMT in DMO (−54 µm, range −482 to 50) than RVO patients (−137 µm, range −478 to 43 p=0.033). Total number of injections received (p=0.028) and final BCVA score (p=0.024) were also significantly different between the groups. Baseline BCVA was a negative predictor (p=0.042) and baseline CMT a positive predictor (p .001) of outcome. After adjusting for baseline BCVA and CMT, diagnosis of nAMD or RVO was a predictor of visual improvement compared with the DMO. At the end of 12 months, nAMD and RVO cohorts had the greatest improvement in BCVA, however the final BCVA for DMO was significantly better than for nAMD.
Publisher: Springer Science and Business Media LLC
Date: 03-2021
DOI: 10.1038/S42003-021-01784-0
Abstract: Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.
Publisher: Springer Science and Business Media LLC
Date: 28-02-2022
DOI: 10.1186/S12886-022-02325-X
Abstract: To assess whether insulin therapy impacts the effectiveness of anti-vascular endothelial growth factor (anti-VEGF) injection for the treatment of diabetic macular edema (DME) in type 2 diabetes mellitus. This was a retrospective multi-center analysis. The best-corrected visual acuity (BCVA) at 12 months, BCVA change, central macular thickness (CMT), CMT change, and cumulative injection number were compared between the insulin and the oral hypoglycemic agent (OHA) groups. The mean final BCVA and CMT improved in both the insulin ( N = 137 p 0.001 p 0.001, respectively) and the OHA group ( N = 61 p = 0.199 p 0.001, respectively). The two treatment groups were comparable for final BCVA ( p = 0.263), BCVA change ( p = 0.184), final CMT ( p = 0.741), CMT change ( p = 0.458), and the cumulative injections received ( p = 0.594). The results were comparable between the two groups when stratified by baseline vision ( p 0.05) and baseline HbA1c ( p 0.05). Insulin therapy does not alter treatment outcomes for anti-VEGF therapy in DME.
Start Date: 2020
End Date: 2020
Funder: Royal Hobart Hospital Research Foundation
View Funded ActivityStart Date: 2020
End Date: 2020
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2018
End Date: 2018
Funder: Multiple Sclerosis Research Australia
View Funded Activity