Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure
Abstract
:1. Introduction
2. Methods
2.1. Editorial Policies and Ethical Considerations
2.2. GWAS Data for IOP
2.3. eQTL Data
2.4. SMR Analysis
2.5. TWAS Analysis
3. Results
3.1. Basic Information of the Summarized Data
3.2. Pleiotropic Association with IOP
3.3. Cis-Regulated Gene Expression in Association with IOP
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Data Source | Total Number of Participants | Number of Eligible Genetic Variants or Probes |
---|---|---|
SMR using GTEx eQTL data | ||
eQTL | 338 | 4543 |
GWAS | 31,269 | 6,432,507 |
SMR using CAGE eQTL data | ||
eQTL | 2765 | 8524 |
GWAS | 31,269 | 6,212,127 |
eQTL Data | Probe | Gene | CHR | Top SNP | PeQTL | PGWAS | Beta | SE | PSMR | PHEIDI | Q Value |
---|---|---|---|---|---|---|---|---|---|---|---|
GTEx | ENSG00000214401.4 | KANSL1-AS1 | 17 | rs199534 | 2.42 × 10−76 | 1.24 × 10−6 | 0.125 | 0.027 | 2.78 × 10−6 | 0.022 | 1.84 × 10−5 |
ENSG00000262500.1 | RP11-259G18.2 | 17 | rs199451 | 2.19 × 10−66 | 1.19 × 10−6 | 0.141 | 0.030 | 2.91 × 10−6 | 0.049 | 1.84 × 10−5 | |
ENSG00000262539.1 | RP11-259G18.3 | 17 | rs199534 | 5.96 × 10−81 | 1.24 × 10−6 | 0.120 | 0.026 | 2.66 × 10−6 | 0.046 | 1.84 × 10−5 | |
ENSG00000175164.9 | ABO | 9 | rs12216891 | 1.20 × 10−22 | 3.70 × 10−7 | 0.208 | 0.046 | 6.40 × 10−6 | 0.412 | 3.04 × 10−5 | |
ENSG00000264070.1 | DND1P1 | 17 | rs112578465 | 1.20 × 10−60 | 5.00 × 10−6 | 0.120 | 0.027 | 1.07 × 10−5 | 0.370 | 4.08 × 10−5 | |
ENSG00000214425.2 | LRRC37A4P | 17 | rs79501144 | 1.11 × 10−102 | 1.04 × 10−5 | −0.115 | 0.027 | 1.57 × 10−5 | 0.526 | 4.50 × 10−5 | |
ENSG00000263503.1 | RP11-707O23.5 | 17 | rs111273167 | 1.88 × 10−75 | 1.08 × 10−5 | 0.118 | 0.028 | 1.90 × 10−5 | 0.530 | 4.50 × 10−5 | |
ENSG00000204650.9 | CRHR1-IT1 | 17 | rs1724390 | 1.21 × 10−53 | 7.53 × 10−6 | 0.251 | 0.058 | 1.66 × 10−5 | 0.893 | 4.50 × 10−5 | |
ENSG00000238083.3 | LRRC37A2 | 17 | rs17426174 | 6.85 × 10−38 | 1.63 × 10−5 | 0.161 | 0.039 | 4.28 × 10−5 | 0.002 | 9.04 × 10−5 | |
ENSG00000196526.6 | AFAP1 | 4 | rs62290601 | 7.45 × 10−80 | 8.11 × 10−5 | −0.096 | 0.025 | 1.12 × 10−4 | 0.030 | 2.12 × 10−4 | |
CAGE | ILMN_1794726 | RNF167 | 17 | rs238243 | 2.22 × 10−175 | 1.23 × 10−5 | 0.147 | 0.034 | 1.53 × 10−5 | 0.627 | 1.48 × 10−4 |
ILMN_2393693 | LRRC37A4 | 17 | rs113661667 | 5.03 × 10−228 | 9.86 × 10−6 | −0.124 | 0.028 | 1.19 × 10−5 | 0.003 | 1.48 × 10−4 | |
ILMN_1784428 | MGC57346 | 17 | rs62057067 | 2.43 × 10−157 | 8.99 × 10−6 | 0.146 | 0.033 | 1.19 × 10−5 | 0.010 | 1.48 × 10−4 | |
ILMN_1680353 | NSF | 17 | rs199442 | 5.94 × 10−15 | 3.84 × 10−7 | 0.612 | 0.144 | 2.11 × 10−5 | 0.108 | 1.53 × 10−4 | |
ILMN_2109343 | SGTB | 5 | rs42884 | 4.56 × 10−137 | 2.68 × 10−5 | −0.159 | 0.038 | 3.45 × 10−5 | 0.015 | 1.67 × 10−4 | |
ILMN_1743621 | C17orf69 | 17 | rs113029914 | 8.60 × 10−34 | 1.01 × 10−5 | 0.334 | 0.081 | 3.32 × 10−5 | 0.005 | 1.67 × 10−4 | |
ILMN_1701998 | AFAP1 | 4 | rs62290601 | 1.26 × 10−179 | 8.11 × 10−5 | −0.127 | 0.033 | 9.23 × 10−5 | 0.009 | 3.35 × 10−4 | |
ILMN_2330845 | NSF | 17 | rs199446 | 1.03 × 10−10 | 7.35 × 10−7 | 0.736 | 0.187 | 8.50 × 10−5 | 0.257 | 3.35 × 10−4 | |
ILMN_1706511 | TEF | 22 | rs4822025 | 1.02 × 10−27 | 5.19 × 10−5 | 0.324 | 0.085 | 1.49 × 10−4 | 0.381 | 4.80 × 10−4 | |
ILMN_1737195 | CENPK | 5 | rs154940 | 3.27 × 10−299 | 1.58 × 10−4 | −0.100 | 0.027 | 1.75 × 10−4 | 0.002 | 5.09 × 10−4 |
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Yang, Z.; Zhang, Z.; Zhu, Y.; Yuan, G.; Yang, J.; Yu, W. Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure. Genes 2023, 14, 1027. https://doi.org/10.3390/genes14051027
Yang Z, Zhang Z, Zhu Y, Yuan G, Yang J, Yu W. Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure. Genes. 2023; 14(5):1027. https://doi.org/10.3390/genes14051027
Chicago/Turabian StyleYang, Zhikun, Zhewei Zhang, Yining Zhu, Guangwei Yuan, Jingyun Yang, and Weihong Yu. 2023. "Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure" Genes 14, no. 5: 1027. https://doi.org/10.3390/genes14051027
APA StyleYang, Z., Zhang, Z., Zhu, Y., Yuan, G., Yang, J., & Yu, W. (2023). Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure. Genes, 14(5), 1027. https://doi.org/10.3390/genes14051027