| Literature DB >> 25277308 |
X Y Liang1, L J Chen1, T K Ng1, J Tuo2, J-L Gao3, P O S Tam1, T Y Y Lai1, C-C Chan2, C P Pang1.
Abstract
PURPOSE: To determine the genetic association of an inflammation-related gene, formyl peptide receptor 1 (FPR1), in exudative age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV).Entities:
Mesh:
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Year: 2014 PMID: 25277308 PMCID: PMC4268466 DOI: 10.1038/eye.2014.226
Source DB: PubMed Journal: Eye (Lond) ISSN: 0950-222X Impact factor: 3.775
Sequence variants detected in FPR1
| 1 | Intron 1 | rs7253284 | c.1-514C>T | — | 1/4/150 | 0/9/161 | 0/16/203 | 0.068 | 0.533 | 6 (1.9) | 9 (2.6) | 16 (3.7) |
| 2 | Intron 1 | rs7253355 | c.1-342C>T | — | 11/54/90 | 14/68/88 | 5/85/129 | 0.070 | 0.020 | 76 (24.5) | 96 (28.2) | 95 (21.7) |
| 3 | Intron 1 | Novel | c.1-55C>T | — | 0/0/153 | 0/0/172 | 0/1/218 | 1.000 | 1.000 | 0 (0.0) | 0 (0.0) | 1 (0.2) |
| 4 | Intron 1 | Novel | c.1-18A>T | — | 0/0/153 | 0/2/170 | 0/0/219 | — | 0.193 | 0 (0.0) | 2 (0.6) | 0 (0.0) |
| 5 | Exon 2 | rs5030878 | c.32T>C | Ile11Thr | 0/6/147 | 0/12/160 | 0/12/207 | 0.491 | 0.540 | 6 (2.0) | 12 (3.5) | 12 (2.7) |
| 6 | Exon 2 | Novel | c.117C>T | Leu39Leu | 0/17/136 | 2/14/156 | 0/18/201 | 0.347 | 0.278 | 17 (5.6) | 18 (5.2) | 18 (4.1) |
| 7 | Exon 2 | Novel | c.279C>T | Phe93Phe | 0/0/153 | 0/0/170 | 0/1/218 | 1.000 | 1.000 | 0 (0.0) | 0 (0.0) | 1 (0.2) |
| 8 | Exon 2 | rs78488639 | c.289C>A | Leu97Met | 0/20/133 | 1/24/144 | 0/15/204 | 0.043 | 0.029 | 20 (6.5) | 26 (7.7) | 15 (3.4) |
| 9 | Exon 2 | rs2070745 | c.301G>C | Val101Leu | 45/75/33 | 60/71/39 | 54/102/63 | 0.261 | 0.066 | 165 (53.9) | 191(56.2) | 210 (47.9) |
| 10 | Exon 2 | rs28930680 | c.306T>C | Phe102Phe | 0/3/150 | 0/1/169 | 0/3/216 | 0.693 | 0.635 | 3 (0.7) | 1 (0.3) | 3 (0.7) |
| 11 | Exon 2 | rs5030879 | c.348C>T | Ile116Ile | 0/2/151 | 0/2/168 | 0/1/218 | 0.571 | 0.583 | 2 (0.7) | 2 (0.6) | 1 (0.2) |
| 12 | Exon 2 | Novel | c.368G>A | Arg123His | 0/1/152 | 0/0/170 | 0/0/219 | 0.411 | — | 1 (0.3) | 0 (0.0) | 0 (0.0) |
| 13 | Exon 2 | Novel | c.439A>T | Ile147Phe | 0/0/155 | 0/2/173 | 0/2/217 | 0.513 | 1.000 | 0 (0.0) | 2 (0.6) | 2 (0.5) |
| 14 | Exon 2 | Novel | c.513G>A | Thr171Thr | 0/0/155 | 0/0/175 | 1/1/217 | 0.491 | 0.448 | 0 (0.0) | 0 (0.0) | 3 (0.7) |
| 15 | Exon 2 | rs2070746 | c.546C>A | Pro182Pro | 37/60/58 | 33/95/47 | 52/108/59 | 0.065 | 0.462 | 134 (43.2) | 161 (46) | 212 (48.4) |
| 16 | Exon 2 | Novel | c.553A>G | Asn185Asp | 0/0/155 | 0/0/175 | 0/2/217 | 0.513 | 0.505 | 0 (0.0) | 0 (0.0) | 2 (0.5) |
| 17 | Exon 2 | rs5030880 | c.568A>T | Arg190Trp | 4/46/105 | 4/63/108 | 6/76/137 | 0.580 | 0.934 | 54 (17.4) | 81 (20.3) | 88 (20.1) |
| 18 | Exon 2 | rs1042229 | c.576T>G | Asn192Lys | — | — | — | — | — | — | — | — |
| — | — | — | c.576T>C | Asn192Asn | — | — | — | — | — | — | — | — |
| 19 | Exon 2 | Novel | c.721C>T | Arg241Trp | 0/0/155 | 0/0/175 | 0/1/218 | 1.000 | 1.000 | 0 (0.0) | 0 (0.0) | 1 (0.2) |
| 20 | Exon 2 | Novel | c.944 G >A | Arg309Gln | 0/0/153 | 0/2/176 | 0/0/220 | — | 0.199 | 0 (0.0) | 2 (0.6) | 0 (0.0) |
| 21 | Exon 2 | rs867228 | c.1037C>A | Glu346Ala | 17/63/73 | 16/81/81 | 17/108/95 | 0.249 | 0.750 | 97 (31.7) | 113 (31.7) | 142 (32.3) |
| 22 | 3′-UTR | Novel | c.1053+8G>T | — | 0/0/153 | 0/0/178 | 0/1/219 | 1.000 | 1.000 | 0 (0.0) | 0 (0.0) | 1 (0.2) |
| 23 | 3′-UTR | rs867341 | c.1053+75A>G | — | 1/7/145 | 0/5/173 | 0/7/213 | 0.378 | 0.829 | 9 (2.9) | 7 (1.4) | 7 (1.6) |
| 24 | 3′-UTR | Novel | c.1053+109G>C | — | 0/1/152 | 0/0/178 | 0/0/220 | 0.410 | — | 5 (1.6) | 0 (0.0) | 0 (0.0) |
| 25 | 3′-UTR | Novel | c.1053+162T>G | — | 0/0/152 | 0/1/170 | 0/0/220 | — | 0.437 | 0 (0.0) | 1 (0.3) | 0 (0.0) |
| 26 | Downstream | rs867229 | c.1053+196C>T | — | 29/50/75 | 18/79/74 | 23/107/87 | 0.0026 | 0.808 | 108 (35.1) | 115 (33.6) | 153 (35.2) |
| 27 | Downstream | rs1868943 | c.1053+205C>T | — | 0/2/152 | 0/0/171 | 0/8/209 | 0.205 | 0.010 | 2 (0.7) | 0 (0.0) | 8 (1.8) |
| 28 | Downstream | Novel | c.1053+219G>A | — | 0/1/153 | 0/3/168 | 0/1/216 | 1.000 | 0.325 | 1 (0.3) | 3 (0.9) | 1 (0.2) |
Genotype frequency presented as number of individual with homozygote/heterozygote/wild-type genotypes
Genotype and allele frequencies of c.576T>G/C is presented in a separate table.
Figure 1Haplotype block structure for the seven common polymorphisms. The haplotype analysis revealed a LD block lying across rs2070746 and rs5030880 in (a) AMD and (b) PCV.
Odds ratios of FPR1-associated polymorphisms
| rs78488639 | c.289C>A | — | — | 0.415 | 1.01 (0.99–1.02) | 1.000 | 0.99 (0.98–1.01) | 0.043 | 2.05 (1.01–4.14) | 0.016 | 2.27 (1.15–4.47) | 0.752 | 0.90 (0.48 –1.71) |
| rs2070745 | c.301G>C | 0.114 | 1.59 (0.89–2.84) | 0.034 | 1.80 (1.04–3.09) | 0.695 | 0.89 (0.49–1.62) | 0.197 | 1.40 (0.84–2.35) | 0.646 | 1.12 (0.68–1.86) | 0.442 | 1.25 (0.71–2.20) |
| rs2070746 | c.546C>A | 0.254 | 0.72 (0.42–1.26) | 0.443 | 0.80 (0.45–1.42) | 0.757 | 0.91 (0.50–1.67) | 0.019 | 0.57 (0.35–0.91) | 0.681 | 1.10 (0.69–1.77) | 0.0086 | 0.51 (0.31–0.85) |
| rs867229 | c.1053+196C>T | 0.234 | 1.46 (0.78–2.74) | 0.813 | 0.92 (0.46–1.84) | 0.173 | 1.59 (0.81–3.11) | 0.0082 | 0.54 (0.34–0.86) | 0.514 | 0.87 (0.57–1.33) | 0.053 | 0.62 (0.39–1.0) |
Note: There was no homozygous genotype of rs78488639 identified in AMD and control group.
Amino-acid substitution prediction of novel rare FPR1 variants
| c.368G>A | R123H | 0/1/152 | 0/0/170 | 0/0/219 | Affect protein function | 0.01 | Probably damaging | 2.753 |
| c.439A>T | I147F | 0/0/155 | 0/2/173 | 0/2/217 | Tolerated | 0.29 | Benign | 0 |
| c.553A>G | N185D | 0/0/155 | 0/0/175 | 0/2/217 | Tolerated | 0.69 | Benign | 0.525 |
| c.721C>T | R241W | 0/0/155 | 0/0/175 | 0/1/218 | Tolerated | 0.09 | Benign | 0.807 |
| c.944G >A | R309Q | 0/0/153 | 0/2/176 | 0/0/220 | Tolerated | 0.22 | Benign | 0.538 |
Combined effects of FPR1 rs78488639 with CFH rs800292 and HTRA1 rs11200638 in exudative AMD and PCV
| P | P | P | |||||
|---|---|---|---|---|---|---|---|
| 1.00 (Ref) | 1.00 (Ref) | 0.317 | 1.52 (0.66–3.49) | 0.0083 | 2.90 (1.29–6.54) | ||
| 2.05 (1.01–4.14) | 0.321 | 3.22 (0.55–18.85) | 0.196 | 3.22 (0.67–15.56) | 0.0062 | 4.83 (1.51–15.51) | |
| 1.00 (Ref) | — | 1.00 (Ref) | 0.090 | 2.01 (0.89–4.55) | 0.020 | 2.58 (1.14–5.84) | |
| 2.27 (1.15–4.47) | 1.000 | 0.91 (0.81–1.01) | 2.22 × 10−4 | 10.47 (2.72–40.29) | 0.019 | 4.03 (1.22–13.28) | |
| 1.01 (0.99–1.02) | — | — | — | — | 0.256 | 1.11 (0.90–1.37) | |
Note: Allele A is the risk allele for FPR1 rs78488639, allele G is risk allele for CFH rs800292, and allele A is the risk allele for HTRA1 rs11200638.
Combined effects of FPR1 rs78488639 with smoking in exudative AMD and PCV
| P | P | ||||
|---|---|---|---|---|---|
| 1.00 (Ref) | — | 1.00 (Ref) | 0.038 | 1.93 (1.04–3.58) | |
| 2.05 (1.01–4.14) | 0.739 | 0.67 (0.16–2.74) | 0.010 | 10.93 (1.30–92.10) | |
| 1.00 (Ref) | — | 1.00 (Ref) | 0.992 | 1.00 (0.48–2.10) | |
| 2.27 (1.15–4.47) | 0.164 | 2.15 (0.72–6.44) | 9.96 × 10−4 | 16.94 (2.06–139.38) | |
| 1.01 (0.99–1.02) | — | — | — | — | |
Note: Allele A is the risk allele for FPR1 rs78488639.