| Literature DB >> 31311124 |
Chandan K Jha1, Rashid Mir2, Imadeldin Elfaki3, Shaheena Banu4, S M S Chahal5.
Abstract
Cardiovascular diseases (CVD) are a major cause of death in India and worldwide. Atherosclerosis is caused by the interaction of environmental and genetic factors. Hypercholesterolemia is an example of a classical risk factor for CVD. The low-density lipoprotein receptor (LDLR) is one of the regulating mechanisms the liver uses for cholesterol homeostasis. Gene variations in the LDLR have been reported to cause hypercholesterolemia and consequently CVD. We investigated the association of polymorphisms in the LDLR (rs5925 and rs1529729) with coronary artery disease (CAD) in 200 coronary artery disease patients and 200 matched healthy controls using allele-specific PCR (AS-PCR). The results indicated that the CT genotype of the rs1529729 polymorphism was associated a decreased susceptibility to CAD with an odds ratio (OR) = 0.42 (95% confidence interval (CI), 0.23-0.77), risk ratio (RR) = 0.59 (0.39-0.89), P = 0.0047. The TT genotype of the rs1529729 polymorphism was also associated with decreased susceptibility to CAD with an OR = 0.19 (95% CI, 0.076-0.47), RR = 0.57 (0.47-0.69), P = 0.0003. The GA genotype of the rs5925 polymorphism was associated with decreased susceptibility to CAD with an OR = 0.45 (95% CI, 0.27-0.75), RR = 0.65 (0.47-0.88), P = 0.002. We concluded that the CT and TT genotypes of the rs1529729 polymorphism and the GA genotype of the rs5925 polymorphism are probably associated with decreased susceptibility to CAD. The simplicity of AS-PCR makes it particularly suitable for the rapid, large-scale screening of gene variabilities in the LDLR. AS-PCR could provide significant benefits in clinical applications with its ability to amplify a lower quantity of samples in a cost-saving manner. Nevertheless, these findings need to be validated in well-designed studies with larger sample sizes and in different populations.Entities:
Keywords: SNPs rs5925 and rs1529729; allele-specific-PCR; atherosclerosis; cardiovascular diseases (CVD); hypercholesterolemia; lipoprotein receptor (LDLR)
Year: 2019 PMID: 31311124 PMCID: PMC6681362 DOI: 10.3390/medsci7070080
Source DB: PubMed Journal: Med Sci (Basel) ISSN: 2076-3271
Primers sequences of allele-specific (AS)-PCR used for genotyping the low-density lipoprotein receptor (LDLR) gene polymorphisms rs1529729 and rs5925.
| SNP | Primer Sequence | Product Size | Ta | |
|---|---|---|---|---|
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| F1 Forward primer (C allele) | 5-GTGGTGCCATGTATAACACCC-3 | 175 bp | 61 °C |
| R1 Reverse primer | 5-CAAGAACCCAAGTTTGGAAAC-3 | |||
| F2 Forward primer (T allele) | 5-GTGGTGCCATGTATAACACCT-3 | 212 bp | ||
| R2 Reverse primer | 5-CTATATCTGGAGGCAAGAACCTGA-3 | |||
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| Reverse primer (G allele) | 5′-GGGTGAGGTTGTGGAAGACG-3′ | 176 bp | 57 °C |
| Reverse primer (A allele) | 5′-GGGTGAGGTTGTGGAAGACA-3′ | 176 bp | ||
| Common Forward primer | 5′-CAGTGTTTAACGGGATTTGT-3′ |
Figure 1The annealing sites of the primers used for genotyping rs1529729 (A) and rs5925 (B).
Figure 2Genotyping of rs1529729 C > T (A) and rs5925 G > A (B) polymorphisms using allele-specific PCR (AS-PCR) assay.
Demographic characteristics of coronary artery disease (CAD) patients and healthy controls.
| Variables | No. of CAD Cases ( | No. of Healthy Controls ( |
|---|---|---|
| No. of cases and controls | 200 (100%) | 200 (100%) |
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| Males | 180 (90%) | 176 (88%) |
| Females | 20 (10%) | 24 (12%) |
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| Age ≤50 | 90 (45%) | 88 (44%) |
| Age >50 | 110 (55%) | 112 (56%) |
Baseline characteristics of CAD patients.
| Variables | CAD Cases ( | (%) |
|---|---|---|
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| ≤140 mg | 129 | (64.5%) |
| >140 mg | 71 | (35.5%) |
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| ≤200 mg | 176 | (88%) |
| >200 mg | 24 | (12%) |
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| ≤40 mg | 166 | (83%) |
| >40 mg | 34 | (17%) |
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| ≤100 mg | 150 | (75%) |
| >100 mg | 50 | (25%) |
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| ≤150 mg | 105 | (52.5%) |
| >150 mg | 95 | (47.5%) |
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| Yes | 15 | (7.5%) |
| No | 185 | (92.5%) |
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| Yes | 29 | (14.5%) |
| No | 171 | (85.5%) |
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| Yes | 39 | (19.5%) |
| No | 161 | (80.5%) |
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| Yes | 121 | (60.5%) |
| No | 79 | (39.5%) |
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| Yes | 71 | (35.5%) |
| No | 129 | (64.5%) |
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| Yes | 4 | (2%) |
| No | 196 | (98%) |
The genotype frequency of the LDLR polymorphisms of study cohorts (controls and CAD patients).
| SNP | Genotype | C/C | C/T | T/T | Chi-Square | Df | |
|---|---|---|---|---|---|---|---|
| rs1529729 | CAD patients | 18 (9%) | 154 (77%) | 28 (14%) | 23.85 | 2 | 0.0001 |
| Controls | 42 (21%) | 152 (76%) | 06 (3%) | ||||
| rs5925 | Genotype | G/G | G/A | A/A | Chi-square | Df | |
| CAD patients | 54 (27%) | 124 (62%) | 22 (11%) | 10.1 | 2 | 0.006 | |
| Controls | 30 (15%) | 152 (76%) | 18 (9%) |
Association of the LDLR rs1529729 C > T and rs5925 G > A gene variations with CAD.
| SNP | Genotypes | Healthy Controls | CAD Cases | Odds Ratio (OR) (95% CI) | Risk Ratio (RR) | |
|---|---|---|---|---|---|---|
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| ( | ( | ||||
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| LDLR-CC | 42 | 18 |
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| LDLR-CT | 152 | 154 | 0.42 (0.23–0.77) | 0.59 (0.39–0.89) | 0.0047 | |
| LDLR-TT | 06 | 28 | 0.09 (0.03–0.26) | 0.36 (0.24–0.55) | 0.0001 | |
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| LDLR-CC | 42 | 18 | 1 (ref.) | 1 (ref.) | ||
| LDLR-(CT + TT) | 158 | 182 | 0.37 (0.21–0.67) | 0.56 (0.38–0.84) | 0.001 | |
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| LDLR-(CC + CT) | 194 | 172 | 1 (ref.) | 1 (ref.) | ||
| LDLR-TT | 06 | 28 | 0.19 (0.076–0.47) | 0.57 (0.47–0.69) | 0.0003 | |
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| LDLR-C | 236 | 190 | 1 (ref.) | 1 (ref.) | ||
| LDLR-T | 164 | 210 | 0.63 (0.47–0.83) | 0.79 (0.69–0.91) | 0.0011 | |
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| LDLR-GG | 30 | 54 | 1 (ref.) | 1 (ref.) | ||
| LDLR-GA | 152 | 124 | 0.45 (0.27–0.75) | 0.65 (0.47–0.88) | 0.002 | |
| LDLR-AA | 18 | 22 | 0.67 (0.32–1.46) | 0.79 (0.50–1.24) | 0.322 | |
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| LDLR-GG | 30 | 54 | 1 (ref.) | 1 (ref.) | ||
| LDLR-(GA+AA) | 170 | 146 | 0.477 (0.28–0.78) | 0.66 (0.48–0.9) | 0.003 | |
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| LDLR-(GG+GA) | 182 | 178 | 1 (ref.) | 1 (ref.) | ||
| LDLR-AA | 18 | 22 | 1.24 (0.64–2.4) | 1.12 (0.78–1.6) | 0.5 | |
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| LDLR-G | 212 | 232 | 1 (ref.) | 1 (ref.) | ||
| LDLR-A | 188 | 168 | 0.8 (0.61–1.07) | 0.9 (0.78–1.03) | 0.107 |
Correlations of the covariates with rs5925 and rs1529729 genotypes.
| rs1529729 | rs5925 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subjects | C/C | C/T | T/T | X2 | DF | G/G | G/A | A/A | X2 | DF | |||
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| Males | 180 | 15 | 138 | 27 | 2.2 | 2 | 0.33 | 48 | 111 | 21 | 0.83 | 2 | 0.66 |
| Females | 20 | 03 | 16 | 01 | 06 | 13 | 01 | ||||||
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| Age ≤ 50 | 90 | 07 | 73 | 10 | 1.61 | 2 | 0.447 | 23 | 58 | 09 | 0.43 | 2 | 0.806 |
| Age > 50 | 110 | 11 | 81 | 18 | 31 | 66 | 13 | ||||||
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| RBS ≤ 140 mg | 129 | 13 | 98 | 18 | 0.52 | 2 | 0.77 | 33 | 83 | 13 | 0.87 | 2 | 0.647 |
| RBS > 140 mg | 71 | 05 | 56 | 10 | 21 | 41 | 09 | ||||||
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| Cholesterol ≤ 200 mg | 176 | 14 | 137 | 25 | 1.96 | 2 | 0.375 | 45 | 114 | 17 | 5.33 | 2 | 0.069 |
| Cholesterol > 200 mg | 24 | 04 | 17 | 03 | 09 | 10 | 05 | ||||||
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| HDL ≤ 40 mg | 166 | 14 | 128 | 24 | 0.5 | 2 | 0.778 | 44 | 104 | 18 | 0.18 | 2 | 0.913 |
| HDL > 40 mg | 34 | 04 | 26 | 04 | 10 | 20 | 04 | ||||||
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| LDL ≤ 100 mg | 150 | 15 | 113 | 22 | 1.07 | 2 | 0.5857 | 44 | 92 | 14 | 2.77 | 2 | 0.25 |
| LDL > 100 mg | 50 | 03 | 41 | 06 | 10 | 32 | 08 | ||||||
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| TGL ≤ 150 mg | 105 | 10 | 79 | 16 | 0.4 | 2 | 0.8187 | 25 | 66 | 14 | 1.95 | 2 | 0.377 |
| TGL > 150 mg | 95 | 08 | 75 | 12 | 29 | 58 | 08 | ||||||
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| Hypertension | 29 | 03 | 22 | 04 | 0.07 | 2 | 0.9656 | 04 | 22 | 03 | 3.26 | 2 | 0.195 |
| No hypertension | 171 | 15 | 132 | 24 | 50 | 102 | 19 | ||||||
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| Diabetes | 39 | 04 | 30 | 05 | 0.13 | 2 | 0.9371 | 07 | 28 | 04 | 2.24 | 2 | 0.326 |
| No diabetes | 161 | 14 | 124 | 23 | 47 | 96 | 18 | ||||||
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| CHD | 15 | 02 | 11 | 02 | 0.37 | 2 | 0.8311 | 01 | 12 | 02 | 3.41 | 2 | 0.181 |
| No CHD | 185 | 16 | 143 | 26 | 53 | 112 | 20 | ||||||
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| Smoking | 121 | 13 | 93 | 15 | 1.6 | 2 | 0.4493 | 26 | 45 | 08 | 2.32 | 2 | 0.313 |
| No smoking | 79 | 05 | 61 | 13 | 28 | 79 | 14 | ||||||
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| Alcohol | 71 | 8 | 52 | 11 | 1.01 | 2 | 0.6035 | 18 | 47 | 06 | 1.07 | 2 | 0.585 |
| No alcohol | 129 | 10 | 102 | 17 | 36 | 77 | 16 | ||||||
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| Pan masala | 04 | 00 | 04 | 00 | 1.22 | 2 | 0.5434 | 00 | 03 | 01 | 1.94 | 2 | 0.379 |
| No pan masala | 196 | 18 | 150 | 28 | 54 | 121 | 21 | ||||||
The rs5925 G > A and rs1529729 C > T genotype distributions in different populations.
| rs5925 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
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| Mexico | Hypertension | 160 | 36 | 22.5 | 73 | 45.63 | 51 | 31.87 | [ |
| Controls | 160 | 34 | 21.25 | 82 | 51.25 | 44 | 27.5 | ||
| Slovenia | Type 2 diabetes | 399 | 67 | 16.8 | 189 | 47.4 | 143 | 35.8 | [ |
| Controls | 196 | 26 | 13.3 | 91 | 46.4 | 79 | 40.3 | ||
| Taiwan | Ischemic stroke | 815 | 52 | 6.4 | 262 | 32.1 | 501 | 61.5 | [ |
| Controls | 430 | 17 | 4 | 146 | 34 | 267 | 62 | ||
| Chile | Hypercholesterolemia | 116 | 25 | 21.6 | 78 | 67.2 | 13 | 11.2 | [ |
| Controls | NA | NA | NA | NA | |||||
| China | Blood pressure | 608 | 297 | 48.8 | 237 | 39 | 74 | 12.2 | [ |
| Controls | 616 | 348 | 56.5 | 216 | 35.1 | 52 | 8.4 | ||
| Present study | CAD | 200 | 54 | 27 | 124 | 62 | 22 | 11 | |
| Controls | 200 | 30 | 15 | 152 | 76 | 18 | 9 | ||
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| rs1529729 | |||||||||
| Iran | CAD | 170 | 43 | 25.44 | 103 | 60.36 | 24 | 14.2 | [ |
| Controls | 104 | 29 | 28.43 | 44 | 42.16 | 31 | 29.41 | ||
| Sweden | Cardiovascular | 5084 | 1610 | 31.7 | 2481 | 48.8 | 993 | 19.5 | [ |
| Controls | NA | NA | NA | NA | |||||
| Present | CAD cases | 200 | 18 | 9 | 154 | 77 | 28 | 14 | |
| study | Controls | 200 | 42 | 21 | 152 | 76 | 6 | 3 |