Genome-wide analysis of genetic pleiotropy and causal genes across three age-related ocular disorders

Alipanahi B, Hormozdiari F, Behsaz B, Cosentino J, McCaw ZR, Schorsch E, Sculley D, Dorfman EH, Foster PJ, Peng LH, Phene S, Hammel N, Carroll A, Khawaja AP, McLean CY (2021) Large-scale machine-learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology. Am J Hum Genet 108:1217–1230. https://doi.org/10.1016/j.ajhg.2021.05.004

Article  CAS  PubMed  PubMed Central  Google Scholar 

Allingham RR, Wiggs JL, Hauser ER, Larocque-Abramson KR, Santiago-Turla C, Broomer B, Del Bono EA, Graham FL, Haines JL, Pericak-Vance MA, Hauser MA (2005) Early adult-onset POAG linked to 15q11-13 using ordered subset analysis. Invest Ophthalmol vis Sci 46:2002–2005. https://doi.org/10.1167/iovs.04-1477

Article  PubMed  Google Scholar 

Andreassen OA, Thompson WK, Schork AJ, Ripke S, Mattingsdal M, Kelsoe JR, Kendler KS, O’Donovan MC, Rujescu D, Werge T, Sklar P, Roddey JC, Chen CH, McEvoy L, Desikan RS, Djurovic S, Dale AM (2013) Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate. PLoS Genet 9:e1003455. https://doi.org/10.1371/journal.pgen.1003455

Article  CAS  PubMed  PubMed Central  Google Scholar 

Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) A global reference for human genetic variation. Nature 526:68–74. https://doi.org/10.1038/nature15393

Article  CAS  PubMed  Google Scholar 

Bhattacharjee S, Rajaraman P, Jacobs KB, Wheeler WA, Melin BS, Hartge P, Yeager M, Chung CC, Chanock SJ, Chatterjee N (2012) A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits. Am J Hum Genet 90:821–835. https://doi.org/10.1016/j.ajhg.2012.03.015

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonelli R, Jackson VE, Prasad A, Munro JE, Farashi S, Heeren TFC, Pontikos N, Scheppke L, Friedlander M, Egan CA, Allikmets R, Ansell BRE, Bahlo M (2021) Identification of genetic factors influencing metabolic dysregulation and retinal support for MacTel, a retinal disorder. Commun Biol 4:274. https://doi.org/10.1038/s42003-021-01788-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bourne R, Steinmetz JD, Flaxman S, Briant PS, Taylor HR, Resnikoff S, Casson RJ, Abdoli A, Abu-Gharbieh E, Afshin AJTLgh (2021) Trends in prevalence of blindness and distance and near vision impairment over 30 years: an analysis for the Global Burden of Disease Study. Lancet Global Health 9:e130–e143

Article  Google Scholar 

Bukhari SM, Kiu KY, Thambiraja R, Sulong S, Rasool AH, Liza-Sharmini AT (2016) Microvascular endothelial function and severity of primary open angle glaucoma. Eye (lond) 30:1579–1587. https://doi.org/10.1038/eye.2016.185

Article  CAS  PubMed  Google Scholar 

Bulik-Sullivan B, Finucane HK, Anttila V, Gusev A, Day FR, Loh PR, Duncan L, Perry JR, Patterson N, Robinson EB, Daly MJ, Price AL, Neale BM (2015) An atlas of genetic correlations across human diseases and traits. Nat Genet 47:1236–1241. https://doi.org/10.1038/ng.3406

Article  CAS  PubMed  PubMed Central  Google Scholar 

Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H (2019) The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 47:D1005-d1012. https://doi.org/10.1093/nar/gky1120

Article  CAS  PubMed  Google Scholar 

Canela-Xandri O, Rawlik K, Tenesa A (2018) An atlas of genetic associations in UK Biobank. Nat Genet 50:1593–1599. https://doi.org/10.1038/s41588-018-0248-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cherry TJ, Yang MG, Harmin DA, Tao P, Timms AE, Bauwens M, Allikmets R, Jones EM, Chen R, De Baere E, Greenberg ME (2020) Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease. Proc Natl Acad Sci U S A 117:9001–9012. https://doi.org/10.1073/pnas.1922501117

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choquet H, Melles RB, Anand D, Yin J, Cuellar-Partida G, Wang W, Hoffmann TJ, Nair KS, Hysi PG, Lachke SA, Jorgenson E (2021) A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects. Nat Commun 12:3595. https://doi.org/10.1038/s41467-021-23873-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cuellar-Partida G, Craig JE, Burdon KP, Wang JJ, Vote BJ, Souzeau E, McAllister IL, Isaacs T, Lake S, Mackey DA, Constable IJ, Mitchell P, Hewitt AW, MacGregor S (2016) Assessment of polygenic effects links primary open-angle glaucoma and age-related macular degeneration. Sci Rep 6:26885. https://doi.org/10.1038/srep26885

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dai Y, Hu R, Liu A, Cho KS, Manuel AM, Li X, Dong X, Jia P, Zhao Z (2022) WebCSEA: web-based cell-type-specific enrichment analysis of genes. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac392

Article  PubMed  PubMed Central  Google Scholar 

de Leeuw CA, Mooij JM, Heskes T, Posthuma D (2015) MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol 11:e1004219. https://doi.org/10.1371/journal.pcbi.1004219

Article  CAS  PubMed  PubMed Central  Google Scholar 

Delahanty RJ, Zhang Y, Bichell TJ, Shen W, Verdier K, Macdonald RL, Xu L, Boyd K, Williams J, Kang JQ (2016) Beyond epilepsy and autism: disruption of GABRB3 causes ocular hypopigmentation. Cell Rep 17:3115–3124. https://doi.org/10.1016/j.celrep.2016.11.067

Article  CAS  PubMed  PubMed Central  Google Scholar 

Durinck S, Spellman PT, Birney E, Huber W (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc 4:1184–1191. https://doi.org/10.1038/nprot.2009.97

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fernández-Sánchez L, Lax P, Campello L, Pinilla I, Cuenca N (2015) Astrocytes and Müller cell alterations during retinal degeneration in a transgenic rat model of retinitis pigmentosa. Front Cell Neurosci 9:484. https://doi.org/10.3389/fncel.2015.00484

Article  CAS  PubMed  PubMed Central  Google Scholar 

Frank RN, Puklin JE, Stock C, Canter LA (2000) Race, iris color, and age-related macular degeneration. Trans Am Ophthalmol Soc 98:109–115 (discussion 115–7)

CAS  PubMed  PubMed Central  Google Scholar 

Freshour SL, Kiwala S, Cotto KC, Coffman AC, McMichael JF, Song JJ, Griffith M, Griffith OL, Wagner AH (2021) Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res 49:D1144-d1151. https://doi.org/10.1093/nar/gkaa1084

Article  CAS  PubMed  Google Scholar 

Fritsche LG, Igl W, Bailey JN, Grassmann F, Sengupta S, Bragg-Gresham JL, Burdon KP, Hebbring SJ, Wen C, Gorski M, Kim IK, Cho D, Zack D, Souied E, Scholl HP, Bala E, Lee KE, Hunter DJ, Sardell RJ, Mitchell P, Merriam JE, Cipriani V, Hoffman JD, Schick T, Lechanteur YT, Guymer RH, Johnson MP, Jiang Y, Stanton CM, Buitendijk GH, Zhan X, Kwong AM, Boleda A, Brooks M, Gieser L, Ratnapriya R, Branham KE, Foerster JR, Heckenlively JR, Othman MI, Vote BJ, Liang HH, Souzeau E, McAllister IL, Isaacs T, Hall J, Lake S, Mackey DA, Constable IJ, Craig JE, Kitchner TE, Yang Z, Su Z, Luo H, Chen D, Ouyang H, Flagg K, Lin D, Mao G, Ferreyra H, Stark K, von Strachwitz CN, Wolf A, Brandl C, Rudolph G, Olden M, Morrison MA, Morgan DJ, Schu M, Ahn J, Silvestri G, Tsironi EE, Park KH, Farrer LA, Orlin A, Brucker A, Li M, Curcio CA, Mohand-Said S, Sahel JA, Audo I, Benchaboune M, Cree AJ, Rennie CA, Goverdhan SV, Grunin M, Hagbi-Levi S, Campochiaro P, Katsanis N, Holz FG, Blond F, Blanche H, Deleuze JF, Igo RP Jr, Truitt B, Peachey NS, Meuer SM, Myers CE, Moore EL, Klein R et al (2016) A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nat Genet 48:134–143. https://doi.org/10.1038/ng.3448

Article  CAS  PubMed  Google Scholar 

Fu DJ, Keenan TD, Faes L, Lim E, Wagner SK, Moraes G, Huemer J, Kern C, Patel PJ, Balaskas K, Sim DA, Bunce C, Stratton I, Keane PA (2021) Insights from survival analyses during 12 years of anti-vascular endothelial growth factor therapy for neovascular age-related macular degeneration. JAMA Ophthalmol 139:57–67. https://doi.org/10.1001/jamaophthalmol.2020.5044

Article  PubMed  Google Scholar 

Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES, Engreitz JM (2019) Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nat Genet 51:1664–1669. https://doi.org/10.1038/s41588-019-0538-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao XR, Huang H, Kim H (2019) Genome-wide association analyses identify 139 loci associated with macular thickness in the UK Biobank cohort. Hum Mol Genet 28:1162–1172. https://doi.org/10.1093/hmg/ddy422

Article  CAS  PubMed  Google Scholar 

García-Bermúdez MY, Freude KK, Mouhammad ZA, van Wijngaarden P, Martin KK, Kolko M (2021) Glial cells in glaucoma: friends, foes, and potential therapeutic targets. Front Neurol 12:624983. https://doi.org/10.3389/fneur.2021.624983

Article  PubMed  PubMed Central  Google Scholar 

Gharahkhani P, Jorgenson E, Hysi P, Khawaja AP, Pendergrass S, Han X, Ong JS, Hewitt AW, Segre AV, Rouhana JM, Hamel AR, Igo RP Jr, Choquet H, Qassim A, Josyula NS, Cooke Bailey JN, Bonnemaijer PWM, Iglesias A, Siggs OM, Young TL, Vitart V, Thiadens A, Karjalainen J, Uebe S, Melles RB, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A, Chen LJ, Rong SS, Aung T, Vithana EN, Consortium N, Consortium A, Biobank Japan p, FinnGen s, Eye UKB, Vision C, group Gs, Me Research T, Tamiya G, Shiga Y, Yamamoto M, Nakazawa T, Currant H, Birney E, Wang X, Auton A, Lupton MK, Martin NG, Ashaye A, Olawoye O, Williams SE, Akafo S, Ramsay M, Hashimoto K, Kamatani Y, Akiyama M, Momozawa Y, Foster PJ, Khaw PT, Morgan JE, Strouthidis NG, Kraft P, Kang JH, Pang CP, Pasutto F, Mitchell P, Lotery AJ, Palotie A, van Duijn C, Haines JL, Hammond C, Pasquale LR, Klaver CCW, Hauser M, Khor CC, Mackey DA, Kubo M, Cheng CY, Craig JE, MacGregor S, Wiggs JL (2021) Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries. Nat Commun 12:1258. https://doi.org/10.1038/s41467-020-20851-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, Plagnol V (2014) Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet 10:e1004383. https://doi.org/10.1371/journal.pgen.1004383

Article  CAS  PubMed 

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