| Literature DB >> 36267411 |
Gang Li1, Zhe Zhang1, Yang Liu1.
Abstract
Background: This study aimed to clarify the relationship between tea consumption and osteoarthritis (OA).Entities:
Keywords: Mendelian randomization; causal association; osteoarthritis; risk factor; tea
Year: 2022 PMID: 36267411 PMCID: PMC9576864 DOI: 10.3389/fgene.2022.1004392
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.772
Characteristics of tea consumption-associated SNPs.
| SNP | Position | EAF | EA | Beta | SE |
| N |
| F-statistic |
|---|---|---|---|---|---|---|---|---|---|
| rs1030510 | 7:17100273 | 0.45 | G | −0.0436 | 0.0069 | 3.6E-10 | 3,49,376 | 0.000114 | 40 |
| rs10741694 | 11:16286183 | 0.63 | C | 0.0404 | 0.0071 | 1.53E-08 | 3,49,376 | 0.0000927 | 32 |
| rs11022751 | 11:13307613 | 0.27 | C | 0.0497 | 0.0078 | 1.83E-10 | 3,49,376 | 0.000116 | 41 |
| rs112476491 | 7:17204040 | 0.03 | A | −0.1186 | 0.0194 | 8.88E-10 | 3,49,376 | 0.000107 | 37 |
| rs11487328 | 1:174601659 | 0.38 | C | −0.0493 | 0.0071 | 5.16E-12 | 3,49,376 | 0.000138 | 48 |
| rs11636222 | 15:75515312 | 0.23 | G | −0.0557 | 0.0089 | 3.79E-10 | 3,49,376 | 0.000112 | 39 |
| rs12591786 | 15:60902512 | 0.16 | T | −0.0609 | 0.0096 | 2.32E-10 | 3,49,376 | 0.000115 | 40 |
| rs12600469 | 17:40834073 | 0.62 | T | 0.0406 | 0.0071 | 1.22E-08 | 3,49,376 | 0.0000936 | 33 |
| rs12901092 | 15:75374145 | 0.39 | A | −0.0654 | 0.0071 | 3.2E-20 | 3,49,376 | 0.000243 | 85 |
| rs12916473 | 15:75321999 | 0.04 | A | 0.1233 | 0.0185 | 2.63E-11 | 3,49,376 | 0.000127 | 44 |
| rs140775622 | 20:62962869 | 0.17 | T | 0.0707 | 0.0099 | 9.33E-13 | 3,49,376 | 0.000146 | 51 |
| rs1481012 | 4:89039082 | 0.11 | G | −0.0778 | 0.0109 | 9.41E-13 | 3,49,376 | 0.000146 | 51 |
| rs149375687 | 5:152034989 | 0.27 | T | −0.0449 | 0.0078 | 7.26E-09 | 3,49,376 | 0.0000948 | 33 |
| rs1601409 | 12:17066769 | 0.46 | G | 0.0382 | 0.0069 | 3.67E-08 | 3,49,376 | 0.0000877 | 31 |
| rs1669433 | 12:11349732 | 0.84 | G | 0.0551 | 0.0093 | 3.33E-09 | 3,49,376 | 0.0001 | 35 |
| rs17645813 | 7:17419697 | 0.08 | A | −0.1058 | 0.013 | 3.32E-16 | 3,49,376 | 0.00019 | 66 |
| rs199621380 | 1:150700614 | 0.41 | G | 0.0413 | 0.007 | 4.53E-09 | 3,49,376 | 0.0000996 | 35 |
| rs200062544 | 7:17260246 | 0.47 | A | 0.049 | 0.007 | 2.64E-12 | 3,49,376 | 0.00014 | 49 |
| rs2315024 | 19:19423817 | 0.33 | A | 0.0434 | 0.0073 | 2.98E-09 | 3,49,376 | 0.000101 | 35 |
| rs2465018 | 6:51241140 | 0.23 | A | 0.0635 | 0.0082 | 1.38E-14 | 3,49,376 | 0.000172 | 60 |
| rs2472297 | 15:75027880 | 0.27 | T | 0.1576 | 0.0078 | 3.82E-91 | 3,49,376 | 0.00117 | 408 |
| rs28548701 | 15:74346021 | 0.8 | C | −0.0502 | 0.0086 | 5.82E-09 | 3,49,376 | 0.0000975 | 34 |
| rs28676340 | 15:75449794 | 0.16 | G | −0.0564 | 0.01 | 1.96E-08 | 3,49,376 | 0.000091 | 32 |
| rs34591452 | 15:74492585 | 0.24 | T | 0.0759 | 0.0081 | 5.48E-21 | 3,49,376 | 0.000251 | 88 |
| rs34606716 | 7:75820449 | 0.24 | A | −0.0453 | 0.0082 | 2.7E-08 | 3,49,376 | 0.0000873 | 31 |
| rs3815455 | 7:75611756 | 0.29 | T | 0.0647 | 0.0076 | 1.74E-17 | 3,49,376 | 0.000207 | 72 |
| rs397074 | 15:74599997 | 0.31 | C | −0.0521 | 0.0075 | 2.8E-12 | 3,49,376 | 0.000138 | 48 |
| rs4410790 | 7:17284577 | 0.63 | C | 0.1215 | 0.0072 | 1.89E-64 | 3,49,376 | 0.000814 | 285 |
| rs4817505 | 21:34343828 | 0.39 | C | 0.0411 | 0.0071 | 6.22E-09 | 3,49,376 | 0.0000959 | 34 |
| rs4887165 | 15:74889356 | 0.81 | C | 0.0539 | 0.0089 | 1.22E-09 | 3,49,376 | 0.000105 | 37 |
| rs60223362 | 7:17459648 | 0.2 | C | −0.0747 | 0.0086 | 5.35E-18 | 3,49,376 | 0.000216 | 75 |
| rs6495129 | 15:75196717 | 0.2 | T | −0.0582 | 0.0086 | 1.35E-11 | 3,49,376 | 0.000131 | 46 |
| rs6697410 | 1:26756209 | 0.74 | T | 0.0436 | 0.0079 | 4.1E-08 | 3,49,376 | 0.0000872 | 30 |
| rs6965666 | 7:17177312 | 0.28 | C | −0.0503 | 0.0078 | 9.14E-11 | 3,49,376 | 0.000119 | 42 |
| rs7174381 | 15:75613289 | 0.31 | C | 0.0522 | 0.0075 | 3.85E-12 | 3,49,376 | 0.000139 | 48 |
| rs73071153 | 7:17545964 | 0.03 | A | −0.1312 | 0.0194 | 1.32E-11 | 3,49,376 | 0.000131 | 46 |
| rs73075157 | 7:17566844 | 0.13 | A | −0.0678 | 0.0103 | 5.42E-11 | 3,49,376 | 0.000124 | 43 |
| rs73169830 | 22:24885208 | 0.08 | C | 0.1027 | 0.0131 | 3.81E-15 | 3,49,376 | 0.000176 | 61 |
| rs73424602 | 22:41461176 | 0.4 | T | −0.0432 | 0.007 | 7.84E-10 | 3,49,376 | 0.000109 | 38 |
| rs77821156 | 7:17331450 | 0.11 | G | 0.0643 | 0.0113 | 1.39E-08 | 3,49,376 | 0.0000927 | 32 |
| rs79217743 | 15:75117912 | 0.14 | T | −0.0602 | 0.0102 | 3.34E-09 | 3,49,376 | 0.0000997 | 35 |
| rs79413667 | 7:17399486 | 0.03 | G | −0.1171 | 0.0201 | 6.03E-09 | 3,49,376 | 0.0000971 | 34 |
| rs79694830 | 7:17286087 | 0.06 | T | 0.0951 | 0.015 | 2.26E-10 | 3,49,376 | 0.000115 | 40 |
| rs7999399 | 13:89233505 | 0.55 | T | 0.0379 | 0.0069 | 4.96E-08 | 3,49,376 | 0.0000863 | 30 |
| rs9624470 | 22:24820268 | 0.58 | A | 0.0729 | 0.007 | 3.06E-25 | 3,49,376 | 0.00031 | 108 |
SNP, single nucleotide polymorphism; EAF, effect allele frequency; EA, effect allele; SE, standard error. The R was calculated as follows: 2 × beta2 × EAF × (1 − EAF)/[2 × beta2 × EAF × (1 − EAF) + se2 × 2 × N × EAF (1 − EAF)]. The F-statistic for each SNP was calculated as follows: F = (N − 2) × R 2/(1 − R 2).
FIGURE 1Forest plots of MR study using genetically predicted tea consumption with OA. Inverse-variance weighted methods, MR–Egger analysis, weighted median, and simple and weighted modes were used in this study.
FIGURE 2Scatter plot of the effect size for each SNP on tea consumption and OA.
MR estimates from each method of the causal effect of tea consumption on osteoarthritis risk.
| MR method | OR | SE | 95% CI |
| Cochran’s Q statistic | Heterogeneity |
|---|---|---|---|---|---|---|
| Inverse variance weighted | 1.19 | 0.04 | 1.08–1.30 | 0.0001 | 35.71 | 0.70 |
| MR-Egger | 1.22 | 0.11 | 0.98–1.53 | 0.077 | 35.81 | 0.73 |
| Maximum likelihood method | 1.23 | 0.07 | 1.06–1.40 | 0.004 | 35.64 | 0.74 |
MR, Mendelian randomization; SNP, single-nucleotide polymorphism; OR, odds ratio; SE, standard error.
FIGURE 3Funnel plot for the causal estimates of each tea SNP with OA.
FIGURE 4Leave-one-out sensitivity analysis for the causal association between tea consumption and OA.
FIGURE 5Forest plot of the effect size for each SNP on tea consumption and OA.