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  1. Article ; Online: Identifying Genetic Biomarkers Predicting Response to Anti-Vascular Endothelial Growth Factor Injections in Diabetic Macular Edema

    Rajya L. Gurung / Liesel M. FitzGerald / Ebony Liu / Bennet J. McComish / Georgia Kaidonis / Bronwyn Ridge / Alex W. Hewitt / Brendan J. Vote / Nitin Verma / Jamie E. Craig / Kathryn P. Burdon

    International Journal of Molecular Sciences, Vol 23, Iss 4042, p

    2022  Volume 4042

    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 ... ...

    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.
    Keywords anti-vascular endothelial growth factor ; diabetic macular edema ; genome-wide association ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 333 ; 616
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Rare, potentially pathogenic variants in 21 keratoconus candidate genes are not enriched in cases in a large Australian cohort of European descent.

    Sionne E M Lucas / Tiger Zhou / Nicholas B Blackburn / Richard A Mills / Jonathan Ellis / Paul Leo / Emmanuelle Souzeau / Bronwyn Ridge / Jac C Charlesworth / Richard Lindsay / Jamie E Craig / Kathryn P Burdon

    PLoS ONE, Vol 13, Iss 6, p e

    2018  Volume 0199178

    Abstract: Many genes have been suggested as candidate genes for keratoconus based on their function, their proximity to associated polymorphisms or due to the identification of putative causative variants within the gene. However, very few of these genes have been ...

    Abstract Many genes have been suggested as candidate genes for keratoconus based on their function, their proximity to associated polymorphisms or due to the identification of putative causative variants within the gene. However, very few of these genes have been assessed for rare variation in keratoconus more broadly. In contrast, VSX1 and SOD1 have been widely assessed, however, the vast majority of studies have been small and the findings conflicting. In a cohort of Australians of European descent, consisting of 385 keratoconus cases and 396 controls, we screened 21 keratoconus candidate genes: BANP, CAST, COL4A3, COL4A4, COL5A1, FOXO1, FNDC3B, HGF, IL1A, IL1B, ILRN, IMMP2L, MPDZ, NFIB, RAB3GAP1, RAD51, RXRA, SLC4A11, SOD1, TF and VSX1. The candidate genes were sequenced in these individuals by either whole exome sequencing or targeted gene sequencing. Variants were filtered to identify rare (minor allele frequency <1%), potentially pathogenic variants. A total of 164 such variants were identified across the two groups with no variants fulfilling these criteria in cases in IL1RN, BANP, IL1B, RAD51 or SOD1. The frequency of variants was compared between cases and controls using chi-square or Fishers' Exact tests for each gene with at least one rare potentially pathogenic variant identified in the case cohort. The number of rare potentially pathogenic variants per gene ranged from three (RXRA) to 102 (MPDZ), however for all genes, there was no difference in the frequency between the cases and controls. We conclude that rare potentially pathogenic variation in the 21 candidate genes assessed do not play a major role in keratoconus susceptibility and pathogenesis.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Identification of a novel MYOC mutation, p.(Trp373*), in a family with open angle glaucoma

    Crawford, April / Andrew Dubowsky / Ashish Agar / Bronwyn Ridge / Emmanuelle Souzeau / Jamie E. Craig / Kathryn P. Burdon

    Gene. 2014 July 25, v. 545

    2014  

    Abstract: MYOC gene variants are associated with autosomal dominant primary open angle glaucoma (POAG). In this study, we describe a previously unreported MYOC variant segregating with a POAG phenotype in an Australian family. Two individuals affected with POAG ... ...

    Abstract MYOC gene variants are associated with autosomal dominant primary open angle glaucoma (POAG). In this study, we describe a previously unreported MYOC variant segregating with a POAG phenotype in an Australian family. Two individuals affected with POAG and three unaffected individuals from the same family were recruited through the Australian and New Zealand Registry of Advanced Glaucoma (ANZRAG). Direct sequencing of all MYOC coding exons identified the novel heterozygous single nucleotide transition MYOC:c.1119G>A, p.(Trp373*), predicted to encode an aberrant truncated MYOC protein in two affected siblings. Two unaffected siblings and an unaffected niece were negative for the MYOC sequence variant.
    Keywords Australians ; exons ; genes ; glaucoma ; heterozygosity ; mutation ; phenotype ; siblings
    Language English
    Dates of publication 2014-0725
    Size p. 271-275.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2014.04.033
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma

    Puya Gharahkhani / Kathryn P. Burdon / Jessica N. Cooke Bailey / Alex W. Hewitt / Matthew H. Law / Louis R. Pasquale / Jae H. Kang / Jonathan L. Haines / Emmanuelle Souzeau / Tiger Zhou / Owen M. Siggs / John Landers / Mona Awadalla / Shiwani Sharma / Richard A. Mills / Bronwyn Ridge / David Lynn / Robert Casson / Stuart L. Graham /
    Ivan Goldberg / Andrew White / Paul R. Healey / John Grigg / Mitchell Lawlor / Paul Mitchell / Jonathan Ruddle / Michael Coote / Mark Walland / Stephen Best / Andrea Vincent / Jesse Gale / Graham RadfordSmith / David C. Whiteman / Grant W. Montgomery / Nicholas G. Martin / David A Mackey / Janey L. Wiggs / Stuart MacGregor / Jamie E. Craig / The NEIGHBORHOOD consortium

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Volume 12

    Abstract: Abstract Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for ...

    Abstract Abstract Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for intraocular pressure (IOP) and optic disc parameters (the overall meta-analysis sample size varying between 32,000 to 48,000 participants), which are glaucoma-related traits. We identified and independently validated four novel genome-wide significant associations within or near MYOF and CYP26A1, LINC02052 and CRYGS, LMX1B, and LMO7 using single variant tests, one additional locus (C9) using gene-based tests, and two genetic pathways - “response to fluid shear stress” and “abnormal retina morphology” - in pathway-based tests. Interestingly, some of the new risk loci contribute to risk of other genetically-correlated eye diseases including myopia and age-related macular degeneration. To our knowledge, this study is the first integrative study to combine genetic data from OAG and its correlated traits to identify new risk variants and genetic pathways, highlighting the future potential of combining genetic data from genetically-correlated eye traits for the purpose of gene discovery and mapping.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2018-02-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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