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      New loci and coding variants confer risk for age-related macular degeneration in East Asians

      research-article
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          Abstract

          Age-related macular degeneration (AMD) is a major cause of blindness, but presents differently in Europeans and Asians. Here, we perform a genome-wide and exome-wide association study on 2,119 patients with exudative AMD and 5,691 controls, with independent replication in 4,226 patients and 10,289 controls, all of East Asian descent, as part of The Genetics of AMD in Asians (GAMA) Consortium. We find a strong association between CETP Asp442Gly (rs2303790), an East Asian-specific mutation, and increased risk of AMD (odds ratio (OR)=1.70, P=5.60 × 10 −22). The AMD risk allele (442Gly), known to protect from coronary heart disease, increases HDL cholesterol levels by 0.17 mmol l −1 ( P=5.82 × 10 −21) in East Asians ( n=7,102). We also identify three novel AMD loci: C6orf223 Ala231Ala (OR=0.78, P=6.19 × 10 −18), SLC44A4 Asp47Val (OR=1.27, P=1.08 × 10 −11) and FGD6 Gln257Arg (OR=0.87, P=2.85 × 10 −8). Our findings suggest that some of the genetic loci conferring AMD susceptibility in East Asians are shared with Europeans, yet AMD in East Asians may also have a distinct genetic signature.

          Abstract

          Age-related macular degeneration (AMD) is a major cause of blindness worldwide. Here, the authors carry out a two-stage genome-wide association study for AMD and identify three new AMD risk loci, highlighting the shared and distinct genetic basis of the disease in East Asians and Europeans.

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          Most cited references31

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          Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration.

          We executed a genome-wide association scan for age-related macular degeneration (AMD) in 2,157 cases and 1,150 controls. Our results validate AMD susceptibility loci near CFH (P < 10(-75)), ARMS2 (P < 10(-59)), C2/CFB (P < 10(-20)), C3 (P < 10(-9)), and CFI (P < 10(-6)). We compared our top findings with the Tufts/Massachusetts General Hospital genome-wide association study of advanced AMD (821 cases, 1,709 controls) and genotyped 30 promising markers in additional individuals (up to 7,749 cases and 4,625 controls). With these data, we identified a susceptibility locus near TIMP3 (overall P = 1.1 x 10(-11)), a metalloproteinase involved in degradation of the extracellular matrix and previously implicated in early-onset maculopathy. In addition, our data revealed strong association signals with alleles at two loci (LIPC, P = 1.3 x 10(-7); CETP, P = 7.4 x 10(-7)) that were previously associated with high-density lipoprotein cholesterol (HDL-c) levels in blood. Consistent with the hypothesis that HDL metabolism is associated with AMD pathogenesis, we also observed association with AMD of HDL-c-associated alleles near LPL (P = 3.0 x 10(-3)) and ABCA1 (P = 5.6 x 10(-4)). Multilocus analysis including all susceptibility loci showed that 329 of 331 individuals (99%) with the highest-risk genotypes were cases, and 85% of these had advanced AMD. Our studies extend the catalog of AMD associated loci, help identify individuals at high risk of disease, and provide clues about underlying cellular pathways that should eventually lead to new therapies.
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            Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations.

            The interpretation of novel missense variants is a challenge with increasing numbers of such variants being identified and a responsibility to report the findings in the context of all available scientific evidence. Various in silico bioinformatic tools have been developed that predict the likely pathogenicity of missense variants; however, their utility within the diagnostic setting requires further investigation. The aim of our study was to test the predictive value of two of these tools, sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen), in a set of 141 missense variants (131 pathogenic, 8 benign) identified in the ABCC8, GCK, and KCNJ11 genes. Sixty-six of the mutations caused a gain of protein function, while 67 were loss-of-function mutations. The evolutionary conservation at each residue was also investigated using multiple sequence alignments from the UCSC genome browser. The sensitivity of SIFT and PolyPhen was reasonably high (69% and 68%, respectively), but their specificity was low (13% and 16%). Both programs were significantly better at predicting loss-of-function mutations than gain-of-function mutations (SIFT, p = 0.001; PolyPhen, p < or = 0.0001). The most reliable method for assessing the likely pathogenicity of a missense variant was to investigate the degree of conservation at the affected residue. Eighty-eight percent of the mutations affected highly conserved residues, while all of the benign variants occurred at residues that were polymorphic across multiple species. Although SIFT and PolyPhen may be useful in prioritizing changes that are likely to cause a loss of protein function, their low specificity means that their predictions should be interpreted with caution and further evidence to support/refute pathogenicity should be sought before reporting novel missense changes.
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              Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease.

              Kawasaki disease is a systemic vasculitis of unknown etiology, with clinical observations suggesting a substantial genetic contribution to disease susceptibility. We conducted a genome-wide association study and replication analysis in 2,173 individuals with Kawasaki disease and 9,383 controls from five independent sample collections. Two loci exceeded the formal threshold for genome-wide significance. The first locus is a functional polymorphism in the IgG receptor gene FCGR2A (encoding an H131R substitution) (rs1801274; P = 7.35 × 10(-11), odds ratio (OR) = 1.32), with the A allele (coding for histadine) conferring elevated disease risk. The second locus is at 19q13, (P = 2.51 × 10(-9), OR = 1.42 for the rs2233152 SNP near MIA and RAB4B; P = 1.68 × 10(-12), OR = 1.52 for rs28493229 in ITPKC), which confirms previous findings(1). The involvement of the FCGR2A locus may have implications for understanding immune activation in Kawasaki disease pathogenesis and the mechanism of response to intravenous immunoglobulin, the only proven therapy for this disease.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                28 January 2015
                : 6
                : 6063
                Affiliations
                [1 ]Singapore Eye Research Institute , Singapore 169856, Singapore
                [2 ]Duke-NUS Graduate Medical School, National University of Singapore , Singapore 169857, Singapore
                [3 ]Department of Ophthalmology, National University of Singapore and National University Health System , Singapore 119228, Singapore
                [4 ]Singapore National Eye Center , Singapore 168751, Singapore
                [5 ]Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine , Kyoto 6068507, Japan
                [6 ]Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong , Hong Kong, China
                [7 ]Department of Ophthalmology, Seoul Metropolitan Government Seoul National University Boramae Medical Center , Seoul 156-707, Korea
                [8 ]Sichuan Provincial Key Laboratory for Human Disease Gene Study, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital , Chengdu 610072, China
                [9 ]School of Medicine, University of Electronic Science and Technology of China , Chengdu 610072, China
                [10 ]Key Laboratory of Vision Loss and Restoration, Ministry of Education of China , Beijing 100044, China
                [11 ]Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases , Beijing 100871, China
                [12 ]Department of Ophthalmology, People’s Hospital, Peking University , Beijing 100871, China
                [13 ]Center for Genomic Medicine/Inserm U.852, Kyoto University Graduate School of Medicine , Kyoto 6068507, Japan
                [14 ]Princess Alexandra Eye Pavilion , Edinburgh EH3 9HA, UK
                [15 ]National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore 308433, Singapore
                [16 ]Division of Human Genetics, Genome Institute of Singapore , Singapore 138672, Singapore
                [17 ]Eye and Retinal Surgeons, Camden Medical Centre , Singapore 248649, Singapore
                [18 ]Saw Swee Hock School of Public Health, National University of Singapore and National University Health System , Singapore 117549, Singapore
                [19 ]Department of Ophthalmology, Saitama Medical University , Iruma 3500495, Japan
                [20 ]Department of Ophthalmology, Faculty of Medicine, University of Yamanashi , Yamanashi 4093898, Japan
                [21 ]Department of Ophthalmology, Tokyo Women’s Medical University Hospital , Tokyo 1628666, Japan
                [22 ]Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine , Kobe 6500017, Japan
                [23 ]Shantou University/Chinese University of Hong Kong Joint Shantou International Eye Center , Shantou 515041, China
                [24 ]Zhongshan Ophthalmic Center, Sun Yat-Sen University , Guangzhou 510060, China
                [25 ]Aier School of Ophthalmology, Central South University , Changsha 410000, China
                [26 ]Department of Ophthalmology, Xin Hua Hospital affiliated to Shanghai Jiao Tong University, School of Medicine , Shanghai 200025, China
                [27 ]Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology , Beijing 100730, China
                [28 ]Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania 15260, USA
                [29 ]Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, USA
                [30 ]Hebrew University, School of Public Health , Jerusalem 91120, Israel
                [31 ]Department of Ophthalmology, Seoul National University Bundang Hospital , Gyeonggi 463-707, Korea
                [32 ]Department of Ophthalmology, University of Sydney and Westmead Millennium Institute , Sydney 2145, Australia
                [33 ]Eye and ENT Hospital of Fudan University , Shanghai 200433, China
                [34 ]BGI-Shenzhen , Shenzhen 518083, China
                [35 ]Ozaki Eye Hospital , Miyazaki 8830066, Japan
                [36 ]Mizoguchi Eye Hospital , Nagasaki 8570016, Japan
                [37 ]Department of Ophthalmology, Kobe City General Hospital , Kobe 6500046, Japan
                [38 ]Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine , Seoul 110-744, Korea
                [39 ]Department of Ophthalmology, School of Medicine, Kyungpook National University , Daegu 700-721, Korea
                [40 ]Department of Ophthalmology, Yeungnam University College of Medicine , Daegu 705-802, Korea
                [41 ]Department of Ophthalmology, College of Medicine, Kosin University , Pusan 606-701, Korea
                [42 ]Department of Ophthalmology, Pusan Paik Hospital, Inje University College of Medicine , Pusan 614-735, Korea
                [43 ]Department of Ophthalmology, Pusan National University Hospital , Pusan 602-739, Korea
                [44 ]Medical Research Institute, Pusan National University , Pusan 602-739, Korea
                [45 ]Department of Pediatrics, National University Health System and National University of Singapore , Singapore 119228, Singapore
                [46 ]Department of Gastroenterology, Asan Medical Center and University of Ulsan College of Medicine , Seoul 138-736, Korea
                [47 ]Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine , Seoul 138-736, Korea
                [48 ]State Key Laboratory of Oncology in Southern China , Guangzhou 510060, China
                [49 ]Department of Experimental Research, Sun Yat-Sen University Cancer Center , Guangzhou 510080, China
                [50 ]Peking Union Medical College, Chinese Academy of Medical Science , Beijing 100730, China
                [51 ]Department of Medicine, National University Health System and National University of Singapore , Singapore 119228, Singapore
                Author notes
                [*]

                These authors contributed equally to this work

                [†]

                These authors jointly supervised this work

                Article
                ncomms7063
                10.1038/ncomms7063
                4317498
                25629512
                c2ed2e5d-bc07-42e0-a31d-5deaf5b867d4
                Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

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                : 21 May 2014
                : 09 December 2014
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