Table 3.
Replication analyses results for the top SNPs associated with age-related macular degeneration (AMD) subphenotypes
|
CNV GA Controls |
Meta-GWAS 1775 819 4134 |
Replication meta-analysis 4515 868 15240 |
Combined analysis 6290 1687 19374 |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Gene | Analysis | EA | OR | P | OR | P | OR | P | Samples† |
| Newly identified SNPs from the discovery analyses | ||||||||||
| rs8091635 | Near BRUNOL4 | CNV vs. control | T | 1.27 | 1.7 × 10−7 | 1.04 | 0.27 | 1.13 | 2.2 × 10−5 | abcdefghijk |
| rs4755455 | Near QSER1 | CNV vs. GA | C | 1.59 | 2.1 × 10−7 | 0.96 | 0.63 | 1.18 | 0.003 | abfghik |
| SNPs previously associated with overall advanced AMD | ||||||||||
| rs10490924 | ARMS2/HTRA1 | CNV vs. GA | T | 1.47 | 4.1 × 10−9 | 1.32 | 1.8 × 10−6 | 1.38 | 7.4 × 10−14 | abcdefghijk |
| rs4711751 | VEGFA | CNV vs. GA | T | 0.99 | 0.86 | 1.12 | 0.04 | 1.07 | 0.13 | abcdefghijk |
| rs9332739 | C2 | CNV vs. GA | C | 1.3 | 0.24 | 1.19 | 0.53 | 1.26 | 0.19 | adeghj |
| rs9621532 | TIMP3 | CNV vs. GA | A | 1.29 | 0.1 | 1.01 | 0.95 | 1.15 | 0.20 | abdeghjk |
| rs13095226 | COL8A1 | CNV vs. GA | T | 1.07 | 0.49 | 1.05 | 0.62 | 1.06 | 0.40 | acdghjk |
| rs10468017 | LIPC | CNV vs. GA | T | 1.01 | 0.94 | 1.04 | 0.52 | 1.04 | 0.52 | abcdefghijk |
| rs1883025 | ABCA1 | CNV vs. GA | T | 1.00 | 0.94 | 0.94 | 0.43 | 0.97 | 0.56 | abcdghijk |
| rs3764261 | CETP | CNV vs. GA | A | 1.13 | 0.054 | 0.93 | 0.21 | 1.02 | 0.59 | abcdefghijk |
| rs1061170 | CFH | CNV vs. GA | T | 1.03 | 0.63 | 1.02 | 0.79 | 1.02 | 0.59 | abcdefghijk |
| rs2230199 | C3 | CNV vs. GA | C | 0.87 | 0.11 | 1.05 | 0.52 | 0.97 | 0.59 | adefghj |
| rs641153 | CFB | CNV vs. GA | A | 0.98 | 0.9 | 0.90 | 0.51 | 0.94 | 0.59 | adeghj |
| rs10033900 | CFI | CNV vs. GA | T | 0.99 | 0.88 | 0.99 | 0.88 | 0.99 | 0.84 | adeghjk |
| rs1999930 | FRK/COL10A1 | CNV vs. GA | T | 1.05 | 0.49 | 0.94 | 0.41 | 0.995 | 0.91 | abcdefghijk |
CNV=choroidal neovascularization, GA= geographic atrophy, SNP = single nucleotide polymorphism, EA= Effective allele (odds ratios are based on this allele), OR= odds ratio, NA=not available
Samples that participated in the combined analysis for each SNP are indicated by letters a to j. “a” represents Tufts/MMAP/MIGen/GAIN (TMMG samples); “b: represents Johns Hopkins University (JHU); “c” represents Washington University (Wash-U); “d” represents Columbia University (COL); “e” represents Rotterdam Study (RS); “f” represents Centre for Eye Research Australia (AUS); “g” represents an independent replication sample from Tufts/Mass General Hospital (Tufts/MGH), “h” represents Hopital Intercommunal de Creteil (FR-CRET); “i” represents the Queen s University of Belfast (Irish); “j” represents the Complications of AMD Prevention Trial (CAPT). Meta-analysis was performed with fixed effects model with inverse-variance weighting.