| Literature DB >> 31915541 |
Tao Li1,2,3, Xian Xu1,2,3, Yi Xu1,2,3, Peiyao Jin1,2,3, Jianhua Chen4, Yongyong Shi5, Haidong Zou1,2,3.
Abstract
OBJECTIVES: To investigate whether the presence of peroxisome proliferator-activated receptor gamma (PPARG) gene polymorphisms is associated with unexplained mild visual impairment (UMVI) in patients with type 2 diabetes mellitus (T2DM).Entities:
Year: 2019 PMID: 31915541 PMCID: PMC6930731 DOI: 10.1155/2019/5284867
Source DB: PubMed Journal: J Ophthalmol ISSN: 2090-004X Impact factor: 1.909
Probe sequence for four SNPs used for Fluidigm sequencing analysis.
| Rs number | SNP | Ch | Functional consequence | Position | SNP_SEQ |
|---|---|---|---|---|---|
| rs10865710 | Intron C>G | 3 | Upstream transcript variant | 12,311,699 | AGTTTCATGTAGGTAAGACTGTGTAGAATGTCGGGTCTCGATGTTGGCGCTATTCAAGCCCTGATGATAAGGCTTTTGGCATTAGATGCTGTTTTGTCTT[C/G]ATGGAAAATACAGCTATTCTAGGATCCTTGAGCCTTTCATAAGAGATAAGGTTGTGAATCCTAAGACCCTAGGACCRTTTACTTAGATGATCTGCTCTCT |
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| rs1801282 | Intron C>G | 3 | Missense variant/coding sequence variant | 12,351,626 | TTGATCTTTTGCTAGATAGAGACAAAATATCAGTGTGAATTACAGCAAACCCCTATTCCATGCTGTTATGGGTGAAACTCTGGGAGATTCTCCTATTGAC[C/G]CAGAAAGCGATTCCTTCACTGATACACTGTCTGCAAACATATCACAAGGTAAAGTTCCTTCCAGATACGGCTATTGGGGACGTGGGGGCATTTATGTAAG |
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| rs709158 | Intron A>G | 3 | Genic downstream transcript variant | 12,403,176 | CTCTGCAGCAGGCAAAAGCTCTTTTTGTTAATTCAAAACAGTTTGGAATCCATTTCAGTTCTTCCTAAACCTCCAAGATACGGGGGAGGAAATTCACTGG[A/G]TTTTACAATATATTTTTCAAGGCAAATTGCCATCGCCGTCCTAATGACAGAGAAGCTGCCGATATCACTACAACGGCTGCAGATGGCAAGTCATCCAGCC |
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| rs3856806 | C1341T | 3 | 3 prime UTR variant/synonymous variant | 12,415,557 | CCCTGGAGCTCCAGCTGAAGCTGAACCACCCTGAGTCCTCACAGCTGTTTGCCAAGCTGCTCCAGAAAATGACAGACCTCAGACAGATTGTCACGGAACA[C/T]GTGCAGCTACTGCAGGTGATCAAGAAGACGGAGACAGACATGAGTCTTCACCYGCTCCTGCAGGAGATCTACAAGGACTTGTACTAGCAGAGAGTCCTGA |
Ch: chromosome.
Demographic and clinical characteristics of 135 residents with unexplained mild visual impairment (UMVI) and 133 residents with normal vision (NV).
| UMVI residents | NV residents |
| |
|---|---|---|---|
| Gender (male) | 53 | 60 | 0.39 |
| Age (year) | 65.34 ± 5.41 | 64.82 ± 8.45 | 0.59 |
| Age at diabetes onset (years) | 58.48 ± 10.76 | 57.51 ± 10.15 | 0.39 |
| Duration of diabetes (years) | 6.86 ± 5.21 | 7.30 ± 5.86 | 0.52 |
| Hemoglobin A1c (%) | 7.24 ± 1.46 | 7.09 ± 1.34 | 0.36 |
| Fasting blood glucose (mmol/l) | 7.21 ± 2.08 | 7.17 ± 1.88 | 0.87 |
| Body mass index (kg/m2) | 25.00 ± 3.62 | 25.75 ± 3.51 | 0.09 |
| Waistline (cm) | 85.68 ± 9.93 | 88.27 ± 9.19 | 0.03 |
| Hipline (cm) | 94.98 ± 9.84 | 97.03 ± 6.77 | 0.04 |
| Systolic blood pressure (mmHg) | 140.02 ± 20.84 | 143.77 ± 19.69 | 0.14 |
| Diastolic blood pressure (mmHg) | 81.03 ± 11.97 | 80.74 ± 11.35 | 0.84 |
Student's t-test and χ2 test.
PPARG allele frequencies in the 135 residents with unexplained mild visual impairment (UMVI) and 133 residents with normal vision (NV).
| SNP | Alleles | UMVI residents | NV residents |
| MAF | OR (95%CI) |
|---|---|---|---|---|---|---|
| number (%) | number (%) | |||||
| rs10865710 | G | 163 (60.4) | 14 (5.3) | 6.57 | 0.33 | 27.42 (15.18–49.51) |
| C | 107 (39.6) | 252 (94.7) | ||||
| rs1801282 | G | 22 (8.1) | 0 (0) | 1.99 | 0.04 | NA |
| C | 248 (91.9) | 266 (100) | ||||
| rs709158 | G | 95 (58.6) | 24 (21.4) | 1.00 | 0.43 | 5.20 (3.00–9.00) |
| A | 67 (41.4) | 88 (78.6) | ||||
| rs3856806 | T | 88 (32.6) | 21 (7.9) | 1.22 | 0.20 | 5.64 (3.38–9.42) |
| C | 182 (67.4) | 245 (92.1) |
MAF = minor allele frequency; OR = odds ratio; CI = confidence interval; NA, the odds ratio was not available where the number of individuals with two copies of the risk allele was zero. χ2 test.
Figure 1PPARG linkage disequilibrium plot of the PPARG single-nucleotide polymorphisms rs3856806, rs1801282, rs709158, and rs10865710. The number in the diamond refers to D0 (100 9 D0). The linkage disequilibrium block was defined according to the standard confidence intervals. The strength of linkage disequilibrium is depicted by the intensity of red coloring, which moves from white to light red as D0 progresses from 0 to 100.
Genotypic association analysis in 135 residents with unexplained mild visual impairment (UMVI) and 133 residents with normal vision (NV).
| SNP | Genotype | UMVI residents | NV residents | HWpval |
| OR (95% CI) |
| OR# (95% CI) |
|---|---|---|---|---|---|---|---|---|
| number | number | |||||||
| rs10865710 | GG | 36 | 0 | 0.08 | 7.17 | NA | ||
| GC | 91 | 14 | 6.40 (3.47–11.80) | 1.86 | 0.01 (0.00–0.02) | |||
| CC | 8 | 119 | 0.07 (0.03–0.14) | (CC: GG + GC) | ||||
| rs1801282 | GG | 0 | 0 | 1 | NA | NA | ||
| GC | 22 | 0 | NA | 7.46 | 0.46 (0.40, 0.53) | |||
| CC | 113 | 133 | 0.86 (0.61–1.21) | (CC: GG + GC) | ||||
| rs709158 | GG | 25 | 4 | 0.33 | 3.35 | 4.43 (1.46–13.43) | 0.41 | 2.22 (0.67, 7.38) |
| GA | 45 | 16 | 1.94 (1.00–3.78) | 6.9 | 20.46 (5.84, 71.61) | |||
| AA | 11 | 36 | 0.21 (0.10–0.45) | 1.39 | 0.11 (0.04, 0.26) | |||
| rs3856806 | TT | 16 | 0 | 0.10 | 1.24 | NA | ||
| TC | 56 | 21 | 2.63 (1.51–4.58) | 8.92 | 0.16 (0.09–0.29) | |||
| CC | 63 | 112 | 0.55 (0.37–0.82) | (CC: TT + TC) |
p value (chi-square test); OR (95% CI) (chi-square test); OR# (95 % CI); p value# (Bonferroni correction); OR' (Bonferroni correction); HWpval, Hardy–Weinberg equilibrium p value. OR = odds ratio; CI = confidence interval; NA, the odds ratio was not available where the number of individuals with two copies of the risk allele was zero. χ2 test.
Haplotype analysis for PPARG SNPs in 135 residents with unexplained mild visual impairment (UMVI) and 133 residents with normal vision (NV).
| rs10865710 | rs1801282 | UMVI residents | NV residents |
| OR (95% CI) |
|---|---|---|---|---|---|
| haplotype frequency | haplotype frequency | ||||
| C | C | 0.34 | 0.95 | 6.57 | 0.04 (0.02–0.07) |
| G | C | 0.52 | 0.05 | 4.04 | 19.67 (10.92–35.45) |
| G | G | 0.08 | 0 | 1.99 | NA |
χ 2 test.