REFERENCES

1. Buniello A, MacArthur JAL, Cerezo M, et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2019;47:D1005-12.

2. Lichou F, Trynka G. Functional studies of GWAS variants are gaining momentum. Nat Commun 2020;11:6283.

3. Fritsche LG, Fariss RN, Stambolian D, Abecasis GR, Curcio CA, Swaroop A. Age-related macular degeneration: genetics and biology coming together. Annu Rev Genomics Hum Genet 2014;15:151-71.

4. Hellstrand K, Hermodsson S. An immunopharmacological analysis of adrenaline-induced suppression of human natural killer cell cytotoxicity. Int Arch Allergy Appl Immunol 1989;89:334-41.

5. Ratnapriya R, Swaroop A. Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing. Genome Med 2013;5:84.

6. Friedman DS, O’Colmain BJ, Muñoz B, et al. Eye Diseases Prevalence Research Group. Prevalence of age-related macular degeneration in the United States. Arch Ophthalmol 2004;122:564-72.

7. Klein R, Peto T, Bird A, Vannewkirk MR. The epidemiology of age-related macular degeneration. Am J Ophthalmol 2004;137:486-95.

8. Ferris FL, Davis MD, Clemons TE, et al. Age-Related Eye Disease Study (AREDS) Research Group. A simplified severity scale for age-related macular degeneration: AREDS Report No. 18. Arch Ophthalmol 2005;123:1570-4.

9. Ambati J, Fowler BJ. Mechanisms of age-related macular degeneration. Neuron 2012;75:26-39.

10. Age-Related Eye Disease Study Research Group. A randomized, placebo-controlled, clinical trial of high-dose supplementation with vitamins C and E, beta carotene, and zinc for age-related macular degeneration and vision loss: AREDS report no. 8. Arch Ophthalmol 2001;119:1417-36.

11. Schultz DW, Klein ML, Humpert AJ, et al. Analysis of the ARMD1 locus: evidence that a mutation in HEMICENTIN-1 is associated with age-related macular degeneration in a large family. Hum Mol Genet 2003;12:3315-23.

12. Swaroop A, Chew EY, Rickman CB, Abecasis GR. Unraveling a multifactorial late-onset disease: from genetic susceptibility to disease mechanisms for age-related macular degeneration. Annu Rev Genomics Hum Genet 2009;10:19-43.

13. Weeks DE, Conley YP, Tsai HJ, et al. Age-related maculopathy: a genomewide scan with continued evidence of susceptibility loci within the 1q31, 10q26, and 17q25 regions. Am J Hum Genet 2004;75:174-89.

14. Klein RJ, Zeiss C, Chew EY, et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005;308:385-9.

15. Edwards AO, Ritter R 3rd, Abel KJ, Manning A, Panhuysen C, Farrer LA. Complement factor H polymorphism and age-related macular degeneration. Science 2005;308:421-4.

16. Haines JL, Hauser MA, Schmidt S, et al. Complement factor H variant increases the risk of age-related macular degeneration. Science 2005;308:419-21.

17. Priya RR, Chew EY, Swaroop A. Genetic studies of age-related macular degeneration: lessons, challenges, and opportunities for disease management. Ophthalmology 2012;119:2526-36.

18. Fritsche LG, Chen W, Schu M, et al. AMD Gene Consortium. Seven new loci associated with age-related macular degeneration. Nat Genet 2013;45:433-9, 439e1-2.

19. Fritsche LG, Igl W, Bailey JN, et al. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nat Genet 2016;48:134-43.

20. Singh N, Swaroop A, Ratnapriya R. Making biological sense of genetic studies of age-related macular degeneration. Adv Exp Med Biol 2021;1256:201-19.

21. Winkler TW, Grassmann F, Brandl C, et al. Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease. BMC Med Genomics 2020;13:120.

22. Zwick ME, Cutler DJ, Chakravarti A. Patterns of genetic variation in Mendelian and complex traits. Annu Rev Genomics Hum Genet 2000;1:387-407.

23. Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015;46:1-30.

24. Raychaudhuri S, Iartchouk O, Chin K, et al. A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet 2011;43:1232-6.

25. Helgason H, Sulem P, Duvvari MR, et al. A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration. Nat Genet 2013;45:1371-4.

26. Seddon JM, Yu Y, Miller EC, et al. Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Nat Genet 2013;45:1366-70.

27. Zhan X, Larson DE, Wang C, et al. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nat Genet 2013;45:1375-9.

28. van de Ven JP, Nilsson SC, Tan PL, et al. A functional variant in the CFI gene confers a high risk of age-related macular degeneration. Nat Genet 2013;45:813-7.

29. Momozawa Y, Akiyama M, Kamatani Y, et al. Low-frequency coding variants in CETP and CFB are associated with susceptibility of exudative age-related macular degeneration in the Japanese population. Hum Mol Genet 2016;25:5027-34.

30. Corominas J, Colijn JM, Geerlings MJ, et al. Whole-exome sequencing in age-related macular degeneration identifies rare variants in COL8A1, a component of Bruch’s membrane. Ophthalmology 2018;125:1433-43.

31. Anderson DH, Radeke MJ, Gallo NB, et al. The pivotal role of the complement system in aging and age-related macular degeneration: hypothesis re-visited. Prog Retin Eye Res 2010;29:95-112.

32. Stanton CM, Yates JR, den Hollander AI, et al. Complement factor D in age-related macular degeneration. Invest Ophthalmol Vis Sci 2011;52:8828-34.

33. Duvvari MR, Paun CC, Buitendijk GH, et al. Analysis of rare variants in the C3 gene in patients with age-related macular degeneration. PLoS One 2014;9:e94165.

34. Yu Y, Triebwasser MP, Wong EK, et al. Whole-exome sequencing identifies rare, functional CFH variants in families with macular degeneration. Hum Mol Genet 2014;23:5283-93.

35. Saksens NT, Geerlings MJ, Bakker B, et al. Rare genetic variants associated with development of age-related macular degeneration. JAMA Ophthalmol 2016;134:287-93.

36. Pietraszkiewicz A, van Asten F, Kwong A, et al. Association of rare predicted loss-of-function variants in cellular pathways with sub-phenotypes in age-related macular degeneration. Ophthalmology 2018;125:398-406.

37. Huang LZ, Li YJ, Xie XF, et al. Whole-exome sequencing implicates UBE3D in age-related macular degeneration in East Asian populations. Nat Commun 2015;6:6687.

38. Geerlings MJ, Kremlitzka M, Bakker B, et al. The functional effect of rare variants in complement genes on C3b degradation in patients with age-related macular degeneration. JAMA Ophthalmol 2017;135:39-46.

39. Wagner EK, Raychaudhuri S, Villalonga MB, et al. Mapping rare, deleterious mutations in Factor H: association with early onset, drusen burden, and lower antigenic levels in familial AMD. Sci Rep 2016;6:31531.

40. Duvvari MR, van de Ven JP, Geerlings MJ, et al. Whole exome sequencing in patients with the cuticular drusen subtype of age-related macular degeneration. PLoS One 2016;11:e0152047.

41. Pras E, Kristal D, Shoshany N, et al. Rare genetic variants in Tunisian Jewish patients suffering from age-related macular degeneration. J Med Genet 2015;52:484-92.

42. Hoffman JD, Cooke Bailey JN, D’Aoust L, et al. Rare complement factor H variant associated with age-related macular degeneration in the Amish. Invest Ophthalmol Vis Sci 2014;55:4455-60.

43. Ratnapriya R, Acar İE, Geerlings MJ, et al. Family-based exome sequencing identifies rare coding variants in age-related macular degeneration. Hum Mol Genet 2020;29:2022-34.

44. Holz FG, Schmitz-Valckenberg S, Fleckenstein M. Recent developments in the treatment of age-related macular degeneration. J Clin Invest 2014;124:1430-8.

45. Nelson MR, Tipney H, Painter JL, et al. The support of human genetic evidence for approved drug indications. Nat Genet 2015;47:856-60.

46. Pennesi ME, Neuringer M, Courtney RJ. Animal models of age related macular degeneration. Mol Aspects Med 2012;33:487-509.

47. Provis JM, Penfold PL, Cornish EE, Sandercoe TM, Madigan MC. Anatomy and development of the macula: specialisation and the vulnerability to macular degeneration. Clin Exp Optom 2005;88:269-81.

48. Adijanto J, Philp NJ. Cultured primary human fetal retinal pigment epithelium (hfRPE) as a model for evaluating RPE metabolism. Exp Eye Res 2014;126:77-84.

49. Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012;337:1190-5.

50. Deplancke B, Alpern D, Gardeux V. The genetics of transcription factor DNA binding variation. Cell 2016;166:538-54.

51. Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 2020;369:1318-30.

52. Strunnikova NV, Maminishkis A, Barb JJ, et al. Transcriptome analysis and molecular signature of human retinal pigment epithelium. Hum Mol Genet 2010;19:2468-86.

53. Pinelli M, Carissimo A, Cutillo L, et al. An atlas of gene expression and gene co-regulation in the human retina. Nucleic Acids Res 2016;44:5773-84.

54. Hoshino A, Ratnapriya R, Brooks MJ, et al. Molecular anatomy of the developing human retina. Dev Cell 2017;43:763-79.e4.

55. Yan W, Peng YR, van Zyl T, et al. Cell atlas of the human fovea and peripheral retina. Sci Rep 2020;10:9802.

56. Sridhar A, Hoshino A, Finkbeiner CR, et al. Single-cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures. Cell Rep 2020;30:1644-59.e4.

57. Cowan CS, Renner M, De Gennaro M, et al. Cell types of the human retina and its organoids at single-cell resolution. Cell 2020;182:1623-40.e34.

58. Voigt AP, Mulfaul K, Mullin NK, et al. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration. Proc Natl Acad Sci U S A 2019;116:24100-7.

59. Liang Q, Dharmat R, Owen L, et al. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling. Nat Commun 2019;10:5743.

60. Gamazon ER, Segrè AV, van de Bunt M, et al. GTEx Consortium. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nat Genet 2018;50:956-67.

61. Ongen H, Brown AA, Delaneau O, Panousis NI, Nica AC, Dermitzakis ET. GTEx Consortium. Estimating the causal tissues for complex traits and diseases. Nat Genet 2017;49:1676-83.

62. Kim-Hellmuth S, Aguet F, Oliva M, et al. GTEx Consortium. Cell type-specific genetic regulation of gene expression across human tissues. Science 2020;369:eaaz8528.

63. Raj T, Rothamel K, Mostafavi S, et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 2014;344:519-23.

64. Watanabe K, Umićević Mirkov M, de Leeuw CA, van den Heuvel MP, Posthuma D. Genetic mapping of cell type specificity for complex traits. Nat Commun 2019;10:3222.

65. Wang X, Park J, Susztak K, Zhang NR, Li M. Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. Nat Commun 2019;10:380.

66. Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 2017;18:220.

67. Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 2015;12:453-7.

68. Fuzik J, Zeisel A, Máté Z, et al. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. Nat Biotechnol 2016;34:175-83.

69. Grün D, Lyubimova A, Kester L, et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 2015;525:251-5.

70. Jaitin DA, Kenigsberg E, Keren-Shaul H, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 2014;343:776-9.

71. Regev A, Teichmann SA, Lander ES, et al. Human Cell Atlas Meeting Participants. The human cell atlas. Elife 2017;6:e27041.

72. Mathys H, Davila-Velderrain J, Peng Z, et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 2019;570:332-7.

73. Agarwal D, Sandor C, Volpato V, et al. A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders. Nat Commun 2020;11:4183.

74. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8.

75. Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019;20:631-56.

76. Wang Y, Navin NE. Advances and applications of single-cell sequencing technologies. Mol Cell 2015;58:598-609.

77. Schaid DJ, Chen W, Larson NB. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat Rev Genet 2018;19:491-504.

78. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010;6:e1000888.

79. Nica AC, Montgomery SB, Dimas AS, et al. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 2010;6:e1000895.

80. Ratnapriya R, Sosina OA, Starostik MR, et al. Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration. Nat Genet 2019;51:606-10.

81. Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015;16:197-212.

82. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet 2009;10:184-94.

83. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008;24:408-15.

84. Hukku A, Pividori M, Luca F, Pique-Regi R, Im HK, Wen X. Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations. Am J Hum Genet 2021;108:25-35.

85. Strunz T, Kiel C, Grassmann F, et al. A mega-analysis of expression quantitative trait loci in retinal tissue. PLoS Genet 2020;16:e1008934.

86. Orozco LD, Chen HH, Cox C, et al. Integration of eQTL and a single-cell atlas in the human eye identifies causal genes for age-related macular degeneration. Cell Rep 2020;30:1246-59.e6.

87. Liu B, Calton MA, Abell NS, et al. Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. Commun Biol 2019;2:186.

88. White MJ, Yaspan BL, Veatch OJ, Goddard P, Risse-Adams OS, Contreras MG. Strategies for pathway analysis using GWAS and WGS data. Curr Protoc Hum Genet 2019;100:e79.

89. Waksmunski AR, Grunin M, Kinzy TG, Igo RP Jr, Haines JL, Cooke Bailey JN. International Age-Related Macular Degeneration Genomics Consortium. Pathway analysis integrating genome-wide and functional data identifies PLCG2 as a candidate gene for age-related macular degeneration. Invest Ophthalmol Vis Sci 2019;60:4041-51.

90. Sekar S, McDonald J, Cuyugan L, et al. Alzheimer’s disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes. Neurobiol Aging 2015;36:583-91.

91. Fromer M, Roussos P, Sieberts SK, et al. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat Neurosci 2016;19:1442-53.

92. Tian L, Kazmierkiewicz KL, Bowman AS, Li M, Curcio CA, Stambolian DE. Transcriptome of the human retina, retinal pigmented epithelium and choroid. Genomics 2015;105:253-64.

93. Newman AM, Gallo NB, Hancox LS, et al. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks. Genome Med 2012;4:16.

94. Pauly D, Agarwal D, Dana N, et al. Cell-type-specific complement expression in the healthy and diseased retina. Cell Rep 2019;29:2835-48.e4.

95. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005;4:Article17.

96. Calabrese GM, Mesner LD, Stains JP, et al. Integrating GWAS and co-expression network data identifies bone mineral density genes SPTBN1 and MARK3 and an osteoblast functional module. Cell Syst 2017;4:46-59.e4.

97. Gustafsson M, Gawel DR, Alfredsson L, et al. A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases. Sci Transl Med 2015;7:313ra178.

98. Mäkinen VP, Civelek M, Meng Q, et al. Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet 2014;10:e1004502.

99. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008;9:559.

100. Gusev A, Ko A, Shi H, et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet 2016;48:245-52.

101. Lawlor DA, Harbord RM, Sterne JAC, Timpson N, Davey Smith G. Mendelian randomization: using genes as instruments for making causal inferences in epidemiology. Statist Med 2008;27:1133-63.

102. Peng YR, Shekhar K, Yan W, et al. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina. Cell 2019;176:1222-37.e22.

103. Menon M, Mohammadi S, Davila-Velderrain J, et al. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun 2019;10:4902.

104. van der Wijst M, de Vries DH, Groot HE, et al. The single-cell eQTLGen consortium. Elife 2020;9:e52155.

105. Sisternes L, Simon N, Tibshirani R, Leng T, Rubin DL. Quantitative SD-OCT imaging biomarkers as indicators of age-related macular degeneration progression. Invest Ophthalmol Vis Sci 2014;55:7093.

106. Niu S, de Sisternes L, Chen Q, Rubin DL, Leng T. Fully automated prediction of geographic atrophy growth using quantitative spectral-domain optical coherence tomography biomarkers. Ophthalmology 2016;123:1737-50.

107. Lai TT, Hsieh YT, Yang CM, Ho TC, Yang CH. Biomarkers of optical coherence tomography in evaluating the treatment outcomes of neovascular age-related macular degeneration: a real-world study. Sci Rep 2019;9:529.

108. Lambert NG, ElShelmani H, Singh MK, et al. Risk factors and biomarkers of age-related macular degeneration. Prog Retin Eye Res 2016;54:64-102.

109. Lauwen S, de Jong EK, Lefeber DJ, den Hollander Al. Omics biomarkers in ophthalmology. Invest Ophthalmol Vis Sci 2017;58:BIO88-98.

110. Kersten E, Paun CC, Schellevis RL, et al. Systemic and ocular fluid compounds as potential biomarkers in age-related macular degeneration. Surv Ophthalmol 2018;63:9-39.

111. Bailey JN, Hoffman JD, Sardell RJ, Scott WK, Pericak-Vance MA, Haines JL. The application of genetic risk scores in age-related macular degeneration: a review. J Clin Med 2016;5:31.

112. Heesterbeek TJ, Lorés-Motta L, Hoyng CB, Lechanteur YTE, den Hollander AI. Risk factors for progression of age-related macular degeneration. Ophthalmic Physiol Opt 2020;40:140-70.

113. Lewis CM, Vassos E. Polygenic risk scores: from research tools to clinical instruments. Genome Med 2020;12:44.

114. Ding Y, Liu Y, Yan Q, et al. AREDS2 Research Group. Bivariate analysis of age-related macular degeneration progression using genetic risk scores. Genetics 2017;206:119-33.

115. Peng Y, Keenan TD, Chen Q, et al. Predicting risk of late age-related macular degeneration using deep learning. NPJ Digit Med 2020;3:111.

116. Yan Q, Weeks DE, Xin H, et al. Deep-learning-based prediction of late age-related macular degeneration progression. Nat Mach Intell 2020;2:141-50.

117. Geerlings MJ, de Jong EK, den Hollander AI. The complement system in age-related macular degeneration: a review of rare genetic variants and implications for personalized treatment. Mol Immunol 2017;84:65-76.

118. Ratnapriya R. Applications of genomic technologies in retinal degenerative diseases. Adv Exp Med Biol 2019;1185:281-5.

119. Handa JT, Bowes Rickman C, Dick AD, et al. A systems biology approach towards understanding and treating non-neovascular age-related macular degeneration. Nat Commun 2019;10:3347.

Journal of Translational Genetics and Genomics
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