| Literature DB >> 32567430 |
Meng Gao1, Kuo Zeng1, Ya Li1, Yong-Ping Liu1, Xi Xia1, Feng-Ling Xu1, Jun Yao1, Bao-Jie Wang1.
Abstract
OBJECTIVE: Schizophrenia is a severe neurodevelopmental disorder with a complex genetic and environmental etiology. The gene encoding EF-hand domain-containing protein D2 (EFHD2) may be a genetic risk locus for schizophrenia.Entities:
Keywords: EFHD2; allele; frequency distribution; genetic polymorphism; genetic risk factor; genotype; haplotype; schizophrenia; single nucleotide polymorphism
Mesh:
Substances:
Year: 2020 PMID: 32567430 PMCID: PMC7309398 DOI: 10.1177/0300060520932801
Source DB: PubMed Journal: J Int Med Res ISSN: 0300-0605 Impact factor: 1.671
EFHD2 gene 5ʹ fragment and 3ʹ fragment.
| Detection target | Location | SNP | Primer sequence | Fragment length (bp) |
|---|---|---|---|---|
| –763 bp ∼ +357 bp | rs71631726 | F5ʹ-GCTATTGTGCCAAGTCATCCGTGTG-3ʹ | 1020 | |
| rs140124965 | R5ʹ-TGAACTCGGTGTAGGGGTTGAAGAC-3ʹ | |||
| +20380 bp ∼ +21040 bp | rs2473357 | F5ʹ-GCTACTTCTTCATTCCGTGGTACGA-3ʹ | 660 | |
| rs10927785 | R5ʹ-GCCTGTGTGTCTCTGGGAGACTTTC-3ʹ |
Abbreviations: SNP, single-nucleotide polymorphism.
Figure 1.Schematic diagram of the distribution of four single-nucleotide polymorphism loci in the EFHD2 gene. Abbreviations: ATG, transcription start site; CDS, coding sequence; UTR, untranslated region.
Genotype and allele frequency distributions and schizophrenia (SCZ) risk for the four single-nucleotide polymorphism loci in EFHD2 in the control and SCZ groups.
| SNP | Genotype | SCZ ( | Control ( |
| OR | 95% CI | ||
|---|---|---|---|---|---|---|---|---|
|
| Frequency (%) |
| Frequency (%) | |||||
| rs71631726 | 0.816 | |||||||
| GG | 208 | 74.02 | 232 | 72.27 | ||||
| GA | 65 | 23.13 | 81 | 25.23 | ||||
| AA | 8 | 2.85 | 8 | 2.49 | ||||
| Per A allele | 81 | 14.41 | 97 | 15.11 | 0.734 | 0.946 | 0.687–1.302 | |
| AA vs. GG | 0.830 | 1.115 | 0.411–3.025 | |||||
| GA vs. GG | 0.563 | 0.895 | 0.614–1.304 | |||||
| (GA+AA) vs. GG | 0.630 | 0.915 | 0.637–1.314 | |||||
| AA vs (GG+GA) | 0.787 | 1.147 | 0.425–3.096 | |||||
| (GG+AA) vs. GA | 0.548 | 0.892 | 0.613–1.297 | |||||
| rs140124965 | 0.137 | |||||||
| −/− | 202 | 71.89 | 212 | 66.04 | ||||
| insC/− | 78 | 27.76 | 104 | 32.40 | ||||
| insC/ insC | 1 | 0.36 | 5 | 1.56 | ||||
| Per insC | 80 | 14.23 | 114 | 17.76 | 0.097 | 0.769 | 0.563–1.050 | |
| insC/ insCvs−/− | 0.217 | 0.214 | 0.024–1.812 | |||||
| insC/− vs. −/− | 0.181 | 0.787 | 0.554–1.118 | |||||
| (insC/−+ insC/ insC) vs. −/− | 0.123 | 0.761 | 0.537–1.077 | |||||
| insC/insC vs. (insC/-+−/−) | 0.139 | 0.226 | 0.026–1.944 | |||||
| (insC/insC+−/−) vs. insC/− | 0.216 | 1.247 | 0.879–1.771 | |||||
| rs2473357 | 0.046 | |||||||
| AA | 195 | 69.40 | 243 | 75.70 | ||||
| AG | 70 | 24.91 | 71 | 22.12 | ||||
| GG | 16 | 5.69 | 7 | 2.18 | ||||
| Per G allele | 102 | 18.15 | 85 | 13.24 | 0.019 | 1.453 | 1.062–1.987 | |
| GG vs. AA | 0.019 | 2.848 | 1.149–7.062 | |||||
| GA vs. AA | 0.288 | 1.229 | 0.840–1.797 | |||||
| (AG+GG) vs. AA | 0.083 | 1.374 | 0.959–1.969 | |||||
| GG vs. (AA+AG) | 0.025 | 2.708 | 1.098–6.682 | |||||
| (AA+GG) vs. AG | 0.420 | 0.856 | 0.587–1.249 | |||||
| rs10927785 | 0.555 | |||||||
| CC | 260 | 92.53 | 298 | 92.83 | ||||
| CT | 18 | 6.41 | 22 | 6.85 | ||||
| TT | 3 | 1.06 | 1 | 0.31 | ||||
| Per T allele | 24 | 4.27 | 24 | 3.74 | 0.638 | 1.149 | 0.645–2.046 | |
| TT vs. CC | 0.345 | 3.438 | 0.355–33.26 | |||||
| CT vs. CC | 0.845 | 0.938 | 0.492–1.787 | |||||
| (TT+CT) vs. CC | 0.885 | 1.046 | 0.566–1.953 | |||||
| TT vs. (CC+CT) | 0.344 | 3.453 | 0.357–33.39 | |||||
| (CC+TT) vs. CT | 0.826 | 1.075 | 0.564–2.048 | |||||
p values were calculated using 2 × 3 and 2 × 2 χ tests (least allele, codominant model, dominant model, recessive model, and superdominant model). A Bonferroni-corrected p < 0.0071 was considered statistically significant. Abbreviations: CI, confidence interval; OR, odds ratio; SCZ, schizophrenia; SNP, single-nucleotide polymorphism.
Distribution of genotype and allele frequencies, frequency distributions, and schizophrenia (SCZ) risk for the four single-nucleotide polymorphism loci in EFHD2 in male control and SCZ subjects.
| SNP | Genotype | Case | Control |
| OR | 95% CI |
|---|---|---|---|---|---|---|
| rs71631726 | 0.980 | |||||
| GG | 100 | 122 | ||||
| GA | 32 | 37 | ||||
| AA | 6 | 7 | ||||
| A | 44 | 51 | 0.844 | 1.045 | 0.674–1.621 | |
| rs140124965 | 0.681 | |||||
| −/− | 105 | 118 | ||||
| −/insC | 32 | 47 | ||||
| InsC/insC | 1 | 1 | ||||
| insC | 34 | 49 | 0.383 | 0.811 | 0.507–1.298 | |
| rs2473357 | 0.035 | |||||
| AA | 89 | 129 | ||||
| AG | 42 | 33 | ||||
| GG | 7 | 4 | ||||
| G | 56 | 41 | 0.008 | 1.807 | 1.164–2.803 | |
| rs10927785 | 0.608 | |||||
| CC | 126 | 156 | ||||
| CT | 10 | 9 | ||||
| TT | 2 | 1 | ||||
| T | 14 | 11 | 0.277 | 1.559 | 0.696–3.493 |
Abbreviations: CI, confidence interval; OR, odds ratio; SNP, single-nucleotide polymorphism.
Figure 2.Linkage disequilibrium diagram of four single-nucleotide polymorphism loci in the EFHD2 gene. The numbers are the multiallelic Dʹ, which represent the level of recombination between the two blocks. (a) schizophrenia group; (b) control group.
Comparison of EFHD2 haplotypes between the schizophrenia and control groups.
| Haplotype block | Haplotype | SCZ ( | Control ( |
| OR | 95% CI | ||
|---|---|---|---|---|---|---|---|---|
|
| % |
| % | |||||
| Block 1 | G/− | |||||||
| All | 405 | 72.2 | 436 | 68.0 | 0.117 | 1.219 | 0.951–1.562 | |
| Male | 200 | 72.7 | 238 | 71.3 | 0.832 | 1.039 | 0.728–1.484 | |
| Female | 205 | 71.5 | 198 | 63.9 | 0.042 | 1.432 | 1.013–2.024 | |
| A/− | ||||||||
| All | 76 | 13.6 | 93 | 16.9 | 0.631 | 0.923 | 0.666–1.280 | |
| Male | 41 | 15.0 | 47 | 14.2 | 0.807 | 1.058 | 0.673–1.664 | |
| Female | 35 | 12.4 | 46 | 14.8 | 0.355 | 0.800 | 0.499–1.283 | |
| G/insC | ||||||||
| All | 75 | 13.4 | 109 | 14.3 | 0.080 | 0.753 | 0.548–1.036 | |
| Male | 31 | 11.4 | 44 | 13.3 | 0.451 | 0.828 | 0.507–1.352 | |
| Female | 44 | 15.6 | 65 | 21.3 | 0.078 | 0.685 | 0.449–1.045 | |
| Block 2 | A/C | |||||||
| All | 459 | 81.7 | 551 | 85.9 | 0.051 | 0.736 | 0.541–1.001 | |
| Male | 220 | 79.7 | 287 | 86.7 | 0.026 | 0.616 | 0.401–0.947 | |
| Female | 239 | 83.5 | 264 | 85.1 | 0.592 | 0.886 | 0.569–1.379 | |
| G/C | ||||||||
| All | 79 | 14.1 | 67 | 10.5 | 0.055 | 1.404 | 0.992–1.987 | |
| Male | 42 | 15.2 | 33 | 10.0 | 0.049 | 1.625 | 0.999–2.647 | |
| Female | 37 | 13.0 | 34 | 11.1 | 0.458 | 1.206 | 0.734–1.981 | |
| G/T | ||||||||
| All | 23 | 4.1 | 17 | 2.7 | 0.163 | 1.569 | 0.829–2.967 | |
| Male | 14 | 3.1 | 8 | 2.3 | 0.080 | 2.164 | 0.894–5.237 | |
| Female | 9 | 5.1 | 9 | 3.1 | 0.862 | 1.087 | 0.425–2.775 | |
Abbreviations: CI, confidence interval; OR, odds ratio; SCZ, schizophrenia.