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Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.

ABSTRACT: Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented through timely diagnosis and treatment. We characterize optic nerve photographs of 67,040 UK Biobank participants and use a multitrait genetic model to identify risk loci for glaucoma. A glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected glaucoma cases and modifies penetrance of the MYOC variant encoding p.Gln368Ter, the most common glaucoma-associated myocilin variant. In the unselected glaucoma population, individuals in the top PRS decile reach an absolute risk for glaucoma 10 years earlier than the bottom decile and are at 15-fold increased risk of developing advanced glaucoma (top 10% versus remaining 90%, odds ratio = 4.20). The PRS predicts glaucoma progression in prospectively monitored, early manifest glaucoma cases (P = 0.004) and surgical intervention in advanced disease (P = 3.6 × 10^-⁶). This glaucoma PRS will facilitate the development of a personalized approach for earlier treatment of high-risk individuals, with less intensive monitoring and treatment being possible for lower-risk groups.

SUBMITTER: Craig JE

PROVIDER: S-EPMC8056672 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.

Craig Jamie E JE Han Xikun X Qassim Ayub A Hassall Mark M Cooke Bailey Jessica N JN Kinzy Tyler G TG Khawaja Anthony P AP An Jiyuan J Marshall Henry H Gharahkhani Puya P Igo Robert P RP Graham Stuart L SL Healey Paul R PR Ong Jue-Sheng JS Zhou Tiger T Siggs Owen O Law Matthew H MH Souzeau Emmanuelle E Ridge Bronwyn B Hysi Pirro G PG Burdon Kathryn P KP Mills Richard A RA Landers John J Ruddle Jonathan B JB Agar Ashish A Galanopoulos Anna A White Andrew J R AJR Willoughby Colin E CE Andrew Nicholas H NH Best Stephen S Vincent Andrea L AL Goldberg Ivan I Radford-Smith Graham G Martin Nicholas G NG Montgomery Grant W GW Vitart Veronique V Hoehn Rene R Wojciechowski Robert R Jonas Jost B JB Aung Tin T Pasquale Louis R LR Cree Angela Jane AJ Sivaprasad Sobha S Vallabh Neeru A NA Viswanathan Ananth C AC Pasutto Francesca F Haines Jonathan L JL Klaver Caroline C W CCW van Duijn Cornelia M CM Casson Robert J RJ Foster Paul J PJ Khaw Peng Tee PT Hammond Christopher J CJ Mackey David A DA Mitchell Paul P Lotery Andrew J AJ Wiggs Janey L JL Hewitt Alex W AW MacGregor Stuart S

Nature genetics 20200120 2

Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented through timely diagnosis and treatment. We characterize optic nerve photographs of 67,040 UK Biobank participants and use a multitrait genetic model to identify risk loci for glaucoma. A glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected glaucoma cases and modifies penetrance of the MYOC variant encoding p.Gln368Ter, the most common glaucoma-associated myocilin variant ...[more]

PMID: 31959993

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Project description:BACKGROUND:Heritability estimates have revealed an important contribution of SNP variants for most common traits; however, SNP analysis by single-trait genome-wide association studies (GWAS) has failed to uncover their impact. In this study, we applied a multitrait GWAS approach to discover additional factor of the missing heritability of human anthropometric variation. METHODS:We analysed 205 traits, including diseases identified at baseline in the GCAT cohort (Genomes For Life- Cohort study of the Genomes of Catalonia) (n=4988), a Mediterranean adult population-based cohort study from the south of Europe. We estimated SNP heritability contribution and single-trait GWAS for all traits from 15?million SNP variants. Then, we applied a multitrait-related approach to study genome-wide association to anthropometric measures in a two-stage meta-analysis with the UK Biobank cohort (n=336?107). RESULTS:Heritability estimates (eg, skin colour, alcohol consumption, smoking habit, body mass index, educational level or height) revealed an important contribution of SNP variants, ranging from 18% to 77%. Single-trait analysis identified 1785 SNPs with genome-wide significance threshold. From these, several previously reported single-trait hits were confirmed in our sample with LINC01432 (p=1.9×10-9) variants associated with male baldness, LDLR variants with hyperlipidaemia (ICD-9:272) (p=9.4×10-10) and variants in IRF4 (p=2.8×10-57), SLC45A2 (p=2.2×10-130), HERC2 (p=2.8×10-176), OCA2 (p=2.4×10-121) and MC1R (p=7.7×10-22) associated with hair, eye and skin colour, freckling, tanning capacity and sun burning sensitivity and the Fitzpatrick phototype score, all highly correlated cross-phenotypes. Multitrait meta-analysis of anthropometric variation validated 27 loci in a two-stage meta-analysis with a large British ancestry cohort, six of which are newly reported here (p value threshold <5×10-9) at ZRANB2-AS2, PIK3R1, EPHA7, MAD1L1, CACUL1 and MAP3K9. CONCLUSION:Considering multiple-related genetic phenotypes improve associated genome signal detection. These results indicate the potential value of data-driven multivariate phenotyping for genetic studies in large population-based cohorts to contribute to knowledge of complex traits.

Dataset Information

Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.

Publications

Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.

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