Genotyping of <i>C3</i> variants in EUGENDA and Rotterdam samples.

<p>Major and minor allele indicated in capital and lower case respectively, MAF: Minor allele frequency, ND: OR could not be determined, NA: Not applicable.</p><p>EUGENDA: a multicenter database comprising participants from Germany and the Netherlands.</p

Rare variants in AMD studies.

<p>NL: The Netherlands, ISL: Iceland, GER: Germany, USA: United states of America, FRA: France.</p><p>NA: Not applicable.</p

Conditional analysis of Arg735Trp for SNPs Arg102Gly/rs2230199 and Pro314Leu/rs1047286.

<p>EUGENDA: a multicenter database comprising participants from the Cologne area, Germany and the Nijmegen area, the Netherlands.</p

Analysis of Rare Variants in the <i>C3</i> Gene in Patients with Age-Related Macular Degeneration

<div><p>Age-related macular degeneration (AMD) is a progressive retinal disorder affecting over 33 million people worldwide. Genome-wide association studies (GWASs) for AMD identified common variants at 19 loci accounting for 15–65% of the heritability and it has been hypothesized that the missing heritability may be attributed to rare variants with large effect sizes. Common variants in the complement component 3 (<i>C3</i>) gene have been associated with AMD and recently a rare <i>C3</i> variant (Lys155Gln) was identified which exerts a large effect on AMD susceptibility independent of the common variants. To explore whether additional rare variants in the <i>C3</i> gene are associated with AMD, we sequenced all coding exons in 84 unrelated AMD cases. Subsequently, we genotyped all identified variants in 1474 AMD cases and 2258 controls. Additionally, because of the known genetic overlap between AMD and atypical hemolytic uremic syndrome (aHUS), we genotyped two recurrent aHUS-associated <i>C3</i> mutations in the entire cohort. Overall, we identified three rare variants (Lys65Gln (<i>P</i> = 0.04), Arg735Trp (OR = 17.4, 95% CI = 2.2–136; <i>P</i> = 0.0003), and Ser1619Arg (OR = 5.2, 95% CI = 1.0–25; <i>P</i> = 0.05) at the <i>C3</i> locus that are associated with AMD in our EUGENDA cohort. However, the Arg735Trp and Ser1619Arg variants were not found to be associated with AMD in the Rotterdam Study. The Lys65Gln variant was only identified in patients from Nijmegen, the Netherlands, and thus may represent a region-specific AMD risk variant.</p></div

<i>C3</i> variants identified by sequence analysis of 84 AMD cases.

<p>Major and minor allele indicated in capital and lower case respectively.</p><p>Reference sequence of <i>C3</i> (NM_000064) gene.</p><p>SIFT: Sorting Intolerant from Tolerant (Intolerance ≤0.05).</p><p>PolyPhen2: Polymorphism Phenotyping (score 0→1).</p

Population characteristics for the individual cohorts.

<p>Population characteristics for the individual cohorts.</p

Regional association results for chromosome 19 SNPs in the <i>PVRL2</i>/<i>APOE</i>/<i>TOMM40</i> gene cluster.

<p>The index, associated SNP is named and shown as a purple diamond (rs2075650: <i>P</i> = 1.1×10⁻⁶).</p

Comparison of effect sizes for early AMD from this study versus published effect estimates for late AMD.

a<p>Superscript shows reference for the largest study reporting genome-wide association of the relevant SNP with late AMD, from which the “Late AMD” effect estimates were derived:</p>1<p>Chen et al, 2010 ¹¹.</p>2<p>Yu et al, 2011 ¹⁵.</p>3<p>Klein et al, 2005 ¹².</p>4<p>Kopplin et al, 2010 ¹³.</p>5<p>Arakawa et al, 2011 ¹⁰.</p>6<p>Neale et al, 2010 ¹⁴.</p>b<p>NCBI Human Genome Build 36.3 coordinates;</p>c<p>Effective allele;</p>d<p>Frequency of the effective allele;</p>e<p>Summary meta-analysis regression coefficient, indicating the overall, estimated change in log(odds) associated with each additional copy of the effective allele;</p>f<p>Estimated odds ratio and 95% confidence interval for each additional copy of the effective allele, based on fixed-effects meta-analysis of European-ancestry cohorts;</p>g<p><i>P</i>-value associated with the estimated OR;</p>h<p>NR: not reported;</p>i<p><i>P</i>-value from test of heterogeneity of regression coefficients between early and advanced AMD. The threshold for study-wise significance was 0.0036, after accounting for multiple tests. Significant results are shown in bold. Heterogeneity could not be assessed for SNPs with no published confidence interval for the late AMD effect estimate;</p>j<p>Ratio of regression coefficient for advanced vs early AMD, formulated as Beta_adv/Beta_early.</p><p><i>Notes:</i> This study did not have data and could not assess association for additional published SNPs rs4711751 in <i>VEGFA</i> and rs11200638 in <i>HTRA1</i>.</p

Results for SNPs showing suggestive evidence of association (<i>P</i>&lt;1×10⁻⁵) in the primary (European-ancestry) meta-analysis of early AMD.

<p>Where multiple correlated SNPs in the same gene/region showed similar association evidence, the most strongly associated SNP is shown.</p>a<p>NCBI Human Genome Build 36.3 coordinates;</p>b<p>Effective allele;</p>c<p>Frequency of the effective allele;</p>d<p>Estimated odds ratio and 95% confidence interval for the effect of each additional copy of the effective allele, based on the fixed-effects, inverse variance-weighted meta-analysis of European-ancestry cohorts;</p>e<p><i>P</i>-value associated with the estimated OR;</p>f<p>Heterogeneity <i>I²</i> statistic;</p>g<p>Heterogeneity <i>P</i>-value, based on Cochran’s Q statistic;</p>h<p>within a 500 kb genomic region centred on the associated SNP.</p

Comparison of estimated effect sizes for early versus advanced AMD for published SNPs showing genome-wide significant association with AMD.

a<p>Superscript shows reference for the largest study reporting genome-wide association of the relevant SNP with AMD:</p>1<p>Chen et al, 2010 ¹¹.</p>2<p>Yu et al, 2011 ¹⁵.</p>3<p>Klein et al, 2005 ¹².</p>4<p>Kopplin et al, 2010 ¹³.</p>5<p>Arakawa et al, 2011 ¹⁰.</p>6<p>Neale et al, 2010 ¹⁴.</p>b<p>NCBI Human Genome Build 36.3 coordinates;</p>c<p>Effective allele;</p>d<p>Frequency of the effective allele;</p>e<p>Summary meta-analysis regression coefficient, indicating the overall, estimated change in log(odds) associated with each additional copy of the effective allele;</p>f<p>Estimated odds ratio and 95% confidence interval for each additional copy of the effective allele, based on fixed-effects meta-analysis of European-ancestry cohorts;</p>g<p><i>P</i>-value associated with the estimated OR;</p>h<p>Heterogeneity <i>P</i>-value, based on Cochran’s Q statistic;</p>i<p><i>P</i>-value from test of heterogeneity of regression coefficients between early and advanced AMD. The threshold for study-wise significance was 0.0024, after accounting for multiple tests. Significant results are shown in bold;</p>j<p>Ratio of regression coefficient for advanced vs early AMD, formulated as Beta_adv/Beta_early.</p><p><i>Notes:</i> This study did not have data and could not assess association for additional published SNPs rs4711751 in <i>VEGFA</i> and rs11200638 in <i>HTRA1</i>.</p