| Literature DB >> 31111662 |
Baoyang Hu1,2, Wenhua Xing2, Feng Li2, Zhi Huang2, Wenkai Zheng2, Demin Ji1,2, Fanglin Niu3, Yong Zhu2, Xuejun Yang2.
Abstract
BACKGROUND: Lumbar disk herniation (LDH) is a degenerative disorder, which partly results from complex genetic factors. The aim of the study was to investigate the potential associations between glypican-6 (GPC6) variants and LDH risk in Han Chinese population.Entities:
Keywords: GPC6 gene; Han Chinese population; case-control study; lumbar disk herniation; polymorphisms
Mesh:
Substances:
Year: 2019 PMID: 31111662 PMCID: PMC6625109 DOI: 10.1002/mgg3.747
Source DB: PubMed Journal: Mol Genet Genomic Med ISSN: 2324-9269 Impact factor: 2.183
Characteristics of cases and controls in this study
| Variable(s) | Cases ( | Controls ( |
|
|---|---|---|---|
| Sex | 0.064 | ||
| Male | 297 | 297 | |
| Female | 211 | 211 | |
| Age, year (mean ± | 48.49 ± 13.71 | 49.16 ± 14.91 | 0.090 |
p < 0.05 indicates statistical significance.
p value obtained using Chi‐squared test.
p value obtained from independent sample t test.
Basic information of candidate SNPs and SNPs functional annotation in HaploReg v4.1 database in this study
| SNP | Alleles | MAF |
| OR | 95% CI |
| Ref | Alt | SNP functional annotation | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| A/B | Case | Control | |||||||||
| rs4773724 | G/T | 0.361 | 0.409 | 0.583 | 0.82 | 0.68 | 0.98 | 0.026 | G | T | Motifs changed |
| rs1008993 | T/C | 0.169 | 0.132 | 1.000 | 1.34 | 1.05 | 1.71 | 0.020 | C | T | DNAse |
| rs9523981 | T/C | 0.382 | 0.349 | 0.205 | 1.15 | 0.96 | 1.38 | 0.125 | C | T | DNAse, Motifs changed |
| rs7320969 | C/G | 0.331 | 0.341 | 1.000 | 0.96 | 0.79 | 1.15 | 0.627 | C | G | Motifs changed |
| rs59624626 | G/T | 0.278 | 0.294 | 0.455 | 0.92 | 0.76 | 1.12 | 0.404 | T | G | DNAse, Motifs changed |
| rs995810 | A/G | 0.183 | 0.186 | 0.240 | 0.98 | 0.78 | 1.22 | 0.847 | A | G | — |
Abbreviations: Alt, Alternation; CI, confidence interval; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; Ref, Reference; SNP, single‐nucleotide polymorphism.
p was calculated by Fisher's exact test.
p was calculated by Chi‐squared test.
p < 0.05 indicates statistical significance.
Genotypic model analysis of relationship between SNPs and LDH risk
| SNP ID | Model | Genotype | Case | Control | OR (95% CI) |
|
|---|---|---|---|---|---|---|
| rs4773724 | Codominant | T/T | 206 | 174 | 1.00 | 0.041 |
| G/T | 237 | 252 | 0.79 (0.60–1.04) | |||
| G/G | 65 | 82 | 0.67 (0.46–0.98) | |||
| Dominant | T/T | 206 | 174 | 1.00 | 0.036 | |
| G/G‐G/T | 302 | 334 | 0.76 (0.59–0.98) | |||
| Recessive | G/T‐T/T | 443 | 426 | 1.00 | 0.136 | |
| G/G | 65 | 82 | 0.77 (0.54–1.09) | |||
| Log‐additive | — | — | — | 0.81 (0.68–0.97) | 0.024 | |
| rs1008993 | Codominant | C/C | 356 | 381 | 1.00 | 0.032 |
| C/T | 132 | 116 | 1.21 (0.91–1.63) | |||
| T/T | 20 | 9 | 2.40 (1.08–5.36) | |||
| Dominant | C/C | 356 | 381 | 1.00 | 0.061 | |
| C/T‐T/T | 152 | 125 | 1.30 (0.99–1.72) | |||
| Recessive | C/T‐C/C | 488 | 497 | 1.00 | 0.042 | |
| T/T | 20 | 9 | 2.29 (1.03–5.08) | |||
| Log‐additive | — | — | — | 1.32 (1.04–1.68) | 0.023 |
Abbreviations: CI, confidence interval; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; SNP, single‐nucleotide polymorphism;
p was calculated by unconditional logistic regression adjusted for age and gender.
p < 0.05 indicates statistical significance.
Stratified analysis of GPC6 polymorphisms by age and risk of LDH
| SNP ID | Model | Genotype | <45 years | >45 years | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | OR (95% CI) |
| Case | Control | OR (95% CI) |
| |||
| rs4773724 | Codominant | T/T | 114 | 83 | 1.00 | 0.015 | 92 | 91 | 1.00 | 0.471 |
| G/T | 102 | 120 | 0.62 (0.42–0.91) | 135 | 132 | 1.00 (0.68–1.46) | ||||
| G/G | 32 | 41 | 0.56 (0.33–0.97) | 33 | 41 | 0.82 (0.47–1.41) | ||||
| Dominant | T/T | 114 | 83 | 1.00 | 0.007 | 92 | 91 | 1.00 | 0.806 | |
| G/G‐G/T | 134 | 161 | 0.60 (0.42–0.87) | 168 | 173 | 0.96 (0.67–1.37) | ||||
| Recessive | G/T‐T/T | 216 | 203 | 1.00 | 0.210 | 227 | 223 | 1.00 | 0.432 | |
| G/G | 32 | 41 | 0.73 (0.44–1.20) | 33 | 41 | 0.82 (0.50–1.35) | ||||
| Log‐additive | — | — | — | 0.72 (0.55–0.93) | 0.011 | — | — | 0.93 (0.72–1.20) | 0.559 | |
| rs9523981 | Codominant | C/C | 83 | 100 | 1.00 | 0.038 | 106 | 108 | 1.00 | 0.816 |
| T/C | 129 | 121 | 1.29 (0.88–1.89) | 121 | 123 | 0.98 (0.67–1.41) | ||||
| T/T | 36 | 23 | 1.89 (1.04–3.44) | 33 | 32 | 1.07 (0.61–1.87) | ||||
| Dominant | C/C | 83 | 100 | 1.00 | 0.083 | 106 | 108 | 1.00 | 0.966 | |
| T/C‐T/T | 165 | 144 | 1.39 (0.96–2.00) | 154 | 155 | 0.99 (0.70–1.41) | ||||
| Recessive | T/C‐C/C | 212 | 221 | 1.00 | 0.085 | 227 | 231 | 1.00 | 0.762 | |
| T/T | 36 | 23 | 1.63 (0.93–2.85) | 33 | 32 | 1.08 (0.64–1.83) | ||||
| Log‐additive | — | — | — | 1.35 (1.03–1.77) | 0.033 | — | — | 1.02 (0.79–1.31) | 0.906 | |
Abbreviations: CI, confidence interval; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; SNP, single‐nucleotide polymorphism.
p was calculated from Wald test adjusted for age and gender.
p < 0.05 indicates statistical significance.
Stratified analysis of GPC6 polymorphisms by sex and risk of LDH
| SNP ID | Model | Genotype | Male | Female | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | OR (95% CI) |
| Case | Control | OR (95% CI) |
| |||
| rs1008993 | Codominant | C/C | 205 | 229 | 1.00 | 0.054 | 151 | 152 | 1.00 | 0.214 |
| T/C | 79 | 62 | 1.42 (0.97–2.09) | 53 | 54 | 0.99 (0.64–1.5) | ||||
| T/T | 13 | 6 | 2.43 (0.91–6.52) | 7 | 3 | 2.39 (0.60–9.42) | ||||
| Dominant | C/C | 205 | 229 | 1.00 | 0.027 | 151 | 152 | 1.00 | 0.780 | |
| T/C‐T/T | 92 | 68 | 1.51 (1.05–2.18) | 60 | 57 | 1.06 (0.69–1.63) | ||||
| Recessive | T/C‐C/C | 284 | 291 | 1.00 | 0.109 | 204 | 206 | 1.00 | 0.212 | |
| T/T | 13 | 6 | 2.23 (0.84–5.96) | 7 | 3 | 2.39 (0.61–9.40) | ||||
| Log‐additive | — | — | — | 1.47 (1.08–2.01) | 0.016 | — | — | 1.13 (0.77–1.65) | 0.528 | |
Abbreviations: CI, confidence interval; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; SNP, single‐nucleotide polymorphism.
p was calculated from Wald test adjusted for age and gender.
p < 0.05 indicates statistical significance.
Figure 1Linkage disequilibrium (LD) analysis of the SNPs on GPC6 Bright red is a significant LD displayed by standard colors schemes. Parameters r2 and D’ were used to analyze LD pattern
the haplotype frequencies of GPC6 polymorphisms and their association with the risk of LDH
| Haplotype | Frequency | OR (95% CI) |
| |
|---|---|---|---|---|
| rs4773724 | rs1008993 | |||
| T | T | 0.169 | 1.32 (1.04–1.68) | 0.020 |
| G | C | 0.361 | 0.81 (0.68–0.97) | 0.023 |
| T | C | 0.531 | 0.95 (0.80–1.14) | 0.589 |
Abbreviations: CI, confidence interval; OR, odds ratio.
p was calculated using unconditional logistic regression analysis with adjustments for gender and age.
p < 0.05 indicates statistical significance.