Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. Genotyping and Sample Quality Control
2.3. Statistical Analysis
2.4. Gene Functional Enrichment, Pathway, and Network Analyses
3. Results
3.1. Clinical Characteristics of the Enrolled Patients
3.2. GWAS and Single-cell eQTL Analysis
3.3. Gene Function and Network Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Variables a | Case (n = 250) | Control (n = 296) | Pb |
---|---|---|---|
Female, N (%) | 146 (58.4) | 154 (52.0) | 0.74 |
Age, years | 59.3 ± 0.8 | 52.1 ± 1.0 | <0.001 |
Hypertension, N (%) | 93 (37.2) | 88 (29.7) | 0.865 |
Diabetes mellitus, N (%) | 17 (6.8) | 37 (12.5) | 0.001 |
Hyperlipidemia, N (%) | 29 (11.6) | 27 (9.1) | 0.476 |
Cigarette smoking, N (%) | 26 (10.4) | 37 (12.5) | 0.615 |
Principal components, mean c | |||
Principal component 1 | 0.0014 | −0.0012 | 0.169 |
Principal component 2 | −0.0002 | 0.0001 | 0.656 |
Principal component 3 | −0.0010 | 0.0008 | 0.039 |
Principal component 4 | −0.0011 | 0.0009 | 0.031 |
Rupture status, N (%) | |||
UIA | 99 (39.6) | - | - |
SAH | 151 (60.4) | - | - |
Gene | Chr. | SNP | Class | M/m a | MAF b | OR c | L95 c | U95 c | Pc | Power d |
---|---|---|---|---|---|---|---|---|---|---|
PRDM2 | 1p36.21 | rs61775135 | intron | C/A | 0.16/0.41 | 0.32 | 0.23 | 0.43 | 3.6E-13 | 0.42 |
GBA | 1q22 | rs75822236 | R535H | C/T | 0.33/0.01 | 161.40 | 53.86 | 483.60 | 1.1E-19 | 1.00 |
FMO4 | 1q24.3 | rs3737926 | F281F | C/T | 0.16/0.37 | 0.36 | 0.27 | 0.50 | 1.8E-10 | 0.32 |
RNF144A | 2p25.1 | rs6741819 | intron | C/T | 0.13/0.37 | 0.25 | 0.18 | 0.36 | 4.0E-14 | 0.72 |
FLJ45964 | 2q37.3 | rs59626274 | stop-gained | C/T | 0.13/0.36 | 0.26 | 0.18 | 0.37 | 5.8E-14 | 0.71 |
LINC01237 | 2q37.3 | rs78458145 | intron | G/A | 0.17/0.4 | 0.24 | 0.17 | 0.35 | 3.1E-15 | 0.68 |
SPCS3 | 4q34.2 | rs17688188 | intergenic | G/A | 0.11/0.33 | 0.27 | 0.19 | 0.38 | 6.0E-13 | 0.73 |
TCF24 | 8q13.1 | rs112859779 | G141S | C/T | 0.1/0.33 | 0.19 | 0.12 | 0.28 | 3.3E-16 | 0.94 |
C9orf92 | 9p22.3 | rs12350582 | intergenic | A/G | 0.33/0.18 | 2.43 | 1.79 | 3.31 | 1.5E-08 | 0.20 |
LINGO2 | 9p21.1 | rs56942085 | intron | G/A | 0.1/0.03 | 6.11 | 3.20 | 11.64 | 3.9E-08 | 0.78 |
TMOD1 | 9q22.33 | rs1052270 | intron | C/T | 0.27/0.42 | 0.41 | 0.30 | 0.56 | 2.7E-08 | 0.15 |
SUSD1 | 9q31.3 | rs79461840 | intron | T/C | 0.13/0.02 | 6.92 | 3.55 | 13.49 | 1.4E-08 | 0.65 |
LINC00474 | 9q33.1 | rs4979583 | intergenic | C/T | 0.41/0.24 | 2.45 | 1.82 | 3.31 | 4.6E-09 | 0.24 |
OLFML2A | 9q33.3 | rs79134766 | A208T | G/A | 0.07/0.37 | 0.14 | 0.09 | 0.21 | 1.7E-19 | 0.96 |
MYEOV | 11q13.3 | rs76855873 | intron | C/T | 0.16/0.37 | 0.33 | 0.24 | 0.46 | 1.2E-11 | 0.43 |
ARHGAP32 | 11q24.3 | rs371331393 | stop-gained | G/A | 0.32/0.02 | 43.57 | 21.84 | 86.95 | 9.3E-27 | 1.00 |
CD163L1 | 12p13.31 | rs138525217 | splice-site | C/T | 0.31/0.01 | 75.98 | 32.13 | 179.70 | 6.2E-23 | 1.00 |
SLC2A14 | 12p13.31 | rs118107419 | intron | C/A | 0.14/0.39 | 0.25 | 0.17 | 0.35 | 1.4E-14 | 0.67 |
DRAM1 | 12q23.2 | rs7964241 e | intergenic | A/G | 0.35/0.21 | 2.49 | 1.81 | 3.42 | 2.0E-08 | 0.25 |
CUL4A | 13q34 | rs74115822 | intergenic | G/A | 0.19/0.03 | 6.25 | 3.58 | 10.90 | 1.1E-10 | 0.80 |
LINC02130 | 16p13.12 | rs11646803 | intron | C/T | 0.28/0.48 | 0.45 | 0.35 | 0.58 | 4.8E-10 | 0.06 |
LOC102724084 | 16q23.2 | rs75861150 | intron | T/C | 0.02/0.16 | 0.14 | 0.07 | 0.28 | 1.3E-08 | 1.00 |
SCARF1 | 17p13.3 | rs3744644 | E639D | G/C | 0.18/0.35 | 0.39 | 0.28 | 0.54 | 6.0E-09 | 0.26 |
MINK1 | 17p13.2 | rs72835045 | intron | G/A | 0.11/0.33 | 0.25 | 0.17 | 0.37 | 1.7E-12 | 0.79 |
SLC47A1 | 17p11.2 | rs2440154 e | intron | G/A | 0.28/0.13 | 2.67 | 1.90 | 3.75 | 1.4E-08 | 0.26 |
NAPA-AS1 | 19q13.32 | rs55800589 | intron | G/C | 0.32/0.4 | 0.38 | 0.29 | 0.49 | 3.4E-13 | 0.23 |
DSCAM | 21q22.2 | rs727333 | intron | C/A | 0.14/0.38 | 0.26 | 0.18 | 0.36 | 3.7E-14 | 0.69 |
LRRC3 | 21q22.3 | rs116969723 | P63P | G/A | 0.11/0.35 | 0.24 | 0.16 | 0.34 | 3.8E-15 | 0.81 |
SLC5A4-AS1 | 22q12.3 | rs117398778 | intron | T/C | 0.21/0.07 | 3.74 | 2.43 | 5.75 | 2.0E-09 | 0.56 |
Biological Function a | Pb | FDR, % b | Gene, N | Gene Set |
---|---|---|---|---|
Biological process in ontology | ||||
GO: 0030154~cell differentiation | 0.0117 | 16.8 | 10 | EDNRA, LINGO2, CUL4A, SLC2A14, MINK1, SCARF1, BOLL, DSCAM, TMOD1, GBA |
GO: 0031175~neuron projection development | 0.0120 | 17.2 | 5 | LINGO2, MINK1, SCARF1, DSCAM, GBA |
GO: 0048468~cell development | 0.0181 | 24.8 | 7 | EDNRA, LINGO2, MINK1, SCARF1, DSCAM, TMOD1, GBA |
GO: 0016358~dendrite development | 0.0192 | 26.1 | 3 | MINK1, SCARF1, DSCAM |
GO: 0048869~cellular developmental process | 0.0209 | 28.1 | 10 | EDNRA, LINGO2, CUL4A, SLC2A14, MINK1, SCARF1, BOLL, DSCAM, TMOD1, GBA |
GO: 0048666~neuron development | 0.0210 | 28.3 | 5 | LINGO2, MINK1, SCARF1, DSCAM, GBA |
GO: 0007275~multicellular organism development | 0.0260 | 33.8 | 11 | EDNRA, LINGO2, CUL4A, SLC2A14, MINK1, PRDM2, SCARF1, BOLL, DSCAM, TMOD1, GBA |
GO: 0051130~positive regulation of cellular component organization | 0.0406 | 47.7 | 5 | LINGO2, CUL4A, SCARF1, DSCAM, GBA |
GO: 0030182~neuron differentiation | 0.0454 | 51.6 | 5 | LINGO2, MINK1, SCARF1, DSCAM, GBA |
Cellular component in ontology | ||||
GO:0044425~membrane part | 0.0088 | 9.7 | 15 | FMO4, RNF144A, LINGO2, EDNRA, LRRC3, ARHGAP32, CD163L1, SLC2A14, SUSD1, SPCS3, MINK1, SLC47A1, DRAM1, SCARF1, DSCAM |
GO:0016021~integral component of membrane | 0.0160 | 16.9 | 13 | FMO4, RNF144A, LINGO2, EDNRA, LRRC3, CD163L1, SLC2A14, SUSD1, SPCS3, SLC47A1, DRAM1, SCARF1, DSCAM |
GO:0031224~intrinsic component of membrane | 0.0186 | 19.4 | 13 | FMO4, RNF144A, LINGO2, EDNRA, LRRC3, CD163L1, SLC2A14, SUSD1, SPCS3, SLC47A1, DRAM1, SCARF1, DSCAM |
GO:0016020~membrane | 0.0205 | 21.1 | 17 | RNF144A, LRRC3, SUSD1, SLC2A14, MINK1, SLC47A1, SCARF1, FMO4, EDNRA, LINGO2, ARHGAP32, CD163L1, SPCS3, DRAM1, DSCAM, TMOD1, GBA |
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Hong, E.P.; Kim, B.J.; Cho, S.S.; Yang, J.S.; Choi, H.J.; Kang, S.H.; Jeon, J.P. Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population. J. Clin. Med. 2019, 8, 275. https://doi.org/10.3390/jcm8020275
Hong EP, Kim BJ, Cho SS, Yang JS, Choi HJ, Kang SH, Jeon JP. Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population. Journal of Clinical Medicine. 2019; 8(2):275. https://doi.org/10.3390/jcm8020275
Chicago/Turabian StyleHong, Eun Pyo, Bong Jun Kim, Steve S. Cho, Jin Seo Yang, Hyuk Jai Choi, Suk Hyung Kang, and Jin Pyeong Jeon. 2019. "Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population" Journal of Clinical Medicine 8, no. 2: 275. https://doi.org/10.3390/jcm8020275
APA StyleHong, E. P., Kim, B. J., Cho, S. S., Yang, J. S., Choi, H. J., Kang, S. H., & Jeon, J. P. (2019). Genomic Variations in Susceptibility to Intracranial Aneurysm in the Korean Population. Journal of Clinical Medicine, 8(2), 275. https://doi.org/10.3390/jcm8020275