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      A multiethnic genome-wide analysis of 44,039 individuals identifies 41 new loci associated with central corneal thickness

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          Abstract

          Central corneal thickness (CCT) is one of the most heritable human traits, with broad-sense heritability estimates ranging between 0.68 to 0.95. Despite the high heritability and numerous previous association studies, only 8.5% of CCT variance is currently explained. Here, we report the results of a multiethnic meta-analysis of available genome-wide association studies in which we find association between CCT and 98 genomic loci, of which 41 are novel. Among these loci, 20 were significantly associated with keratoconus, and one ( RAPSN rs3740685) was significantly associated with glaucoma after Bonferroni correction. Two-sample Mendelian randomization analysis suggests that thinner CCT does not causally increase the risk of primary open-angle glaucoma. This large CCT study explains up to 14.2% of CCT variance and increases substantially our understanding of the etiology of CCT variation. This may open new avenues of investigation into human ocular traits and their relationship to the risk of vision disorders.

          Abstract

          Hélène Choquet et al. report the largest genome-wide analysis of central corneal thickness (CCT) to date, finding novel associations at 41 loci. The study, which includes individuals from 4 ethnic groups, including African Americans and Hispanic/Latino individuals, increases the variance explained for CCT from 8.5% to 14.2%. Study findings also suggest that thinner CCT does not causally increase the risk of primary open-angle glaucoma.

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          Global consensus on keratoconus and ectatic diseases.

          Despite extensive knowledge regarding the diagnosis and management of keratoconus and ectatic corneal diseases, many controversies still exist. For that reason, there is a need for current guidelines for the diagnosis and management of these conditions. This project aimed to reach consensus of ophthalmology experts from around the world regarding keratoconus and ectatic diseases, focusing on their definition, concepts, clinical management, and surgical treatments. The Delphi method was followed with 3 questionnaire rounds and was complemented with a face-to-face meeting. Thirty-six panelists were involved and allocated to 1 of 3 panels: definition/diagnosis, nonsurgical management, or surgical treatment. The level of agreement considered for consensus was two thirds. Numerous agreements were generated in definitions, methods of diagnosing, and management of keratoconus and other ectatic diseases. Nonsurgical and surgical treatments for these conditions, including the use of corneal cross-linking and corneal transplantations, were presented in a stepwise approach. A flowchart describing a logical management sequence for keratoconus was created. This project resulted in definitions, statements, and recommendations for the diagnosis and management of keratoconus and other ectatic diseases. It also provides an insight into the current worldwide treatment of these conditions.
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            UK biobank data: come and get it.

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              VEGAS2: Software for More Flexible Gene-Based Testing.

              Gene-based tests such as versatile gene-based association study (VEGAS) are commonly used following per-single nucleotide polymorphism (SNP) GWAS (genome-wide association studies) analysis. Two limitations of VEGAS were that the HapMap2 reference set was used to model the correlation between SNPs and only autosomal genes were considered. HapMap2 has now been superseded by the 1,000 Genomes reference set, and whereas early GWASs frequently ignored the X chromosome, it is now commonly included. Here we have developed VEGAS2, an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. VEGAS2 allows greater flexibility when defining gene boundaries. VEGAS2 offers both a user-friendly, web-based front end and a command line Linux version. The online version of VEGAS2 can be accessed through https://vegas2.qimrberghofer.edu.au/. The command line version can be downloaded from https://vegas2.qimrberghofer.edu.au/zVEGAS2offline.tgz. The command line version is developed in Perl, R and shell scripting languages; source code is available for further development.
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                Author and article information

                Contributors
                Helene.Choquet@kp.org
                Eric.Jorgenson@kp.org
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                11 June 2020
                11 June 2020
                2020
                : 3
                : 301
                Affiliations
                [1 ]ISNI 0000 0000 9957 7758, GRID grid.280062.e, Kaiser Permanente Northern California (KPNC), Division of Research, ; Oakland, CA 94612 USA
                [2 ]KPNC, Department of Ophthalmology, Redwood City, CA 94063 USA
                [3 ]ISNI 0000 0001 2297 6811, GRID grid.266102.1, Institute for Human Genetics, University of California San Francisco (UCSF), ; San Francisco, CA 94143 USA
                [4 ]ISNI 0000 0001 2297 6811, GRID grid.266102.1, Department of Epidemiology and Biostatistics, UCSF, ; San Francisco, CA 94158 USA
                [5 ]ISNI 0000000121901201, GRID grid.83440.3b, UCL Institute of Ophthalmology, University College London, ; London, UK
                [6 ]ISNI 0000000121901201, GRID grid.83440.3b, National Institute of Health Research Biomedical Research Centre for Ophthalmology, and UCL Institute of Ophthalmology, ; London, UK
                [7 ]ISNI 0000 0000 8726 5837, GRID grid.439257.e, Moorfields Eye Hospital, ; London, UK
                [8 ]ISNI 0000 0001 2297 6811, GRID grid.266102.1, Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, ; San Francisco, CA 94143 USA
                [9 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, King’s College London, Section of Ophthalmology, School of Life Course Sciences, ; London, UK
                [10 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, King’s College London, Department of Twin Research and Genetic Epidemiology, ; London, UK
                [11 ]ISNI 0000000121901201, GRID grid.83440.3b, University College London, Great Ormond Street Hospital Institute of Child Health, ; London, UK
                Author information
                http://orcid.org/0000-0001-9839-8667
                http://orcid.org/0000-0001-6893-4449
                http://orcid.org/0000-0002-0038-6770
                http://orcid.org/0000-0003-2644-055X
                http://orcid.org/0000-0001-5752-2510
                http://orcid.org/0000-0002-5829-8191
                Article
                1037
                10.1038/s42003-020-1037-7
                7289804
                32528159
                43fcc055-dd10-4773-a160-53f81c80fe40
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 15 January 2020
                : 22 May 2020
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                © The Author(s) 2020

                genome-wide association studies,anatomy
                genome-wide association studies, anatomy

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