Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Declaration
2.2. Study Population
2.3. Study Design
2.4. SNVs Selection
2.5. DNA Extraction
2.6. Genotyping
2.7. Sequencing
2.8. Statistical Analysis
3. Results
3.1. Genotype and Allelic Distribution of SNVs
3.2. Haplotype Analysis
4. Discussion
5. Conclusions
6. Study Limitations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gen/SNP | Allele/ Genotype | Cases | Controls | χ2 | p-Value | ||
---|---|---|---|---|---|---|---|
(n = 114) | (n = 456) | ||||||
N | Frequency | n | Frequency | ||||
TLR1 (rs5743618) | A | 166 | 0.73 | 647 | 0.71 | 0.309 | 0.5778 |
C | 62 | 0.27 | 265 | 0.29 | |||
A/A | 61 | 0.54 | 231 | 0.51 | 0.314 | 0.8543 * | |
A/C | 44 | 0.39 | 185 | 0.41 | |||
C/C | 9 | 0.08 | 40 | 0.09 | |||
TLR2 (rs5743708) | G | 227 | 1 | 909 | 1 | 0.062 | 0.8022 * |
A | 1 | 0 | 3 | 0 | |||
G/A | 1 | 0.01 | 3 | 0.01 | 0.062 | 0.8019 | |
G/G | 113 | 0.99 | 453 | 0.99 | |||
TLR6 (rs5743810) | G | 194 | 0.85 | 738 | 0.81 | 2.12 | 0.1451 |
A | 34 | 0.15 | 174 | 0.19 | |||
A/A | 3 | 0.03 | 14 | 0.03 | 2.57 | 0.2760 | |
G/A | 28 | 0.25 | 146 | 0.32 | |||
G/G | 83 | 0.73 | 296 | 0.65 |
Gene/SNV | Model | Genotype | Cases | Controls | OR (95% CI) | p-Value * |
---|---|---|---|---|---|---|
n (Frequency) | n (Frequency) | |||||
TLR1 rs5743618 | Codominant | A/A | 61 | 231 (50.7%) | 1 | 0.99 |
−53.50% | ||||||
C/A | 44 | 185 (40.6%) | 0.98 (0.60–1.59) | |||
−38.60% | ||||||
C/C | 9 | 40 | 0.95 (0.40–2.25) | |||
−7.90% | −8.80% | |||||
Dominant | A/A | 61 (53.5%) | 231 (50.7%) | 1 | 0.91 | |
C/A-C/C | 53 | 225 (49.3%) | 0.97 (0.61–1.54) | |||
−46.50% | ||||||
Recessive | A/A-C/A | 105 (92.1%) | 416 (91.2%) | 1 | 0.92 | |
C/C | 9 | 40 (8.8%) | 0.96 (0.41–2.21) | |||
−7.90% | ||||||
Over-dominant | A/A-C/C | 70 (61.4%) | 271 (59.4%) | 1 | 0.95 | |
C/A | 44 (38.6%) | 185 (40.6%) | 0.99 (0.62–1.58) | |||
Log-additive | --- | --- | --- | 0.98 (0.68–1.40) | 0.89 | |
TLR6 rs5743810 | Codominant | G/G | 83 (72.8%) | 296 (64.9%) | 1 | 0.18 |
A/G | 28 (24.6%) | 146 (32%) | 0.61 (0.6–1.04) | |||
A/A | 3 (2.6%) | 14 (3.1%) | 0.75 (0.18–3.04) | |||
Dominant | G/G | 83 (72.8%) | 296 (64.9%) | 1 | 0.066 | |
A/G-A/A | 31 (27.2%) | 160 (35.1%) | 0.63 (0.38–1.04) | |||
Recessive | G/G-A/G | 111 (97.4%) | 442 (96.9%) | 1 | 0.83 | |
A/A | 3 (2.6%) | 14 (3.1%) | 0.86 (0.21–3.47) | |||
Over-dominant | G/G-A/A | 86 (75.4%) | 310 (68%) | 1 | 0.07 | |
A/G | 28 (24.6%) | 146 (32%) | 0.62 (0.37–1.05) | |||
Log-additive | --- | --- | 1.46 (0.93–2.29) | 0.68 (0.44–1.08) | 0.092 |
Gene/SNV | Model | Genotype | Cases n (Frequency) | Controls n (Frequency) | OR (95% CI) | p-Value * |
---|---|---|---|---|---|---|
TLR1 rs5743618 | Codominant | A/A | 32 (55.2%) | 107 (46.7%) | 1 | 0.46 |
C/A | 22 (37.9%) | 100 (43.7%) | 0.68 (0.33–1.41) | |||
C/C | 4 (6.9%) | 22 (9.6%) | 0.54 (0.14–2.06) | |||
Dominant | A/A | 32 (55.2%) | 107 (46.7%) | 1 | 0.23 | |
C/A-C/C | 26 (44.8%) | 122 (53.3%) | 0.66 (0.33–1.31) | |||
Recessive | A/A-C/A | 54 (93.1%) | 207 (90.4%) | 1 | 0.5 | |
C/C | 4 (6.9%) | 22 (9.6%) | 0.65 (0.18–2.35) | |||
Over-dominant | A/A-C/C | 36 (62.1%) | 129 (56.3%) | 1 | 0.4 | |
C/A | 22 (37.9%) | 100 (43.7%) | 0.74 (0.37–1.50) | |||
Log-additive | --- | --- | --- | 0.71 (0.41–1.23) | 0.22 | |
TLR6 rs5743810 | Codominant | G/G | 45 (77.6%) | 147 (64.2%) | 1 | 0.049 |
A/G | 11 (19%) | 74 (32.3%) | 0.37 (0.16–0.86) | |||
A/A | 2 (3.5%) | 8 (3.5%) | 0.56 (0.09–3.52) | |||
Dominant | G/G | 45 (77.6%) | 147 (64.2%) | 1 | 0.016 | |
A/G-A/A | 13 (22.4%) | 82 (35.8%) | 0.39 (0.17–0.87) | |||
Recessive | G/G-A/G | 56 (96.5%) | 221 (96.5%) | 1 | 0.74 | |
A/A | 2 (3.5%) | 8 (3.5%) | 0.74 (0.12–4.53) | |||
Over-dominant | G/G-A/A | 47 (81%) | 155 (67.7%) | 1 | 0.019 | |
A/G | 11 (19%) | 74 (32.3%) | 0.38 (0.16–0.88) | |||
Log-additive | --- | --- | --- | 0.49 (0.25–0.97) | 0.032 |
Haplotype | rs5743618 | rs5743708 | rs5743810 | Frequency | OR (95% CI) | p-Value * |
---|---|---|---|---|---|---|
1 | A | G | G | 0.7044 | 1 | --- |
2 | C | G | A | 0.1756 | 0.65 (0.40–1.06) | 0.082 |
3 | C | G | G | 0.1096 | 1.86 (1.11–3.10) | 0.019 |
Female Subgroup, n = 283. | ||||||
---|---|---|---|---|---|---|
Haplotype | rs5743618 | rs5743708 | rs5743810 | Frequency | OR (95% CI) | p-Value * |
1 | A | G | G | 0.71 | 1 | --- |
2 | C | G | A | 0.17 | 0.81 (0.42–1.59) | 0.55 |
3 | C | G | G | 0.10 | 2.39 (1.21–4.72) | 0.013 |
4 | A | rs5743708 G | A | 0.01 | 6.92 (1.08–44.25) | 0.042 |
Global haplotype association p-value: 0.017 | ||||||
Male Subgroup, n = 287. | ||||||
Haplotype | rs5743618 | rs5743708 | rs5743810 | Frequency | OR (95% CI) | p-value * |
1 | A | G | G | 0.6928 | 1 | --- |
2 | C | G | A | 0.181 | 0.51 (0.25–1.01) | 0.056 |
3 | C | G | G | 0.1207 | 1.32 (0.59–2.93) | 0.5 |
Global haplotype association p-value: 0.15 |
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Gutierrez-Castañeda, L.D.; Acosta, C.R.; Bustos, M.A.; García, D.K.; Bohada, D.P.; Rodríguez, R.; Guerrero, M.I. Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population. Trop. Med. Infect. Dis. 2023, 8, 473. https://doi.org/10.3390/tropicalmed8100473
Gutierrez-Castañeda LD, Acosta CR, Bustos MA, García DK, Bohada DP, Rodríguez R, Guerrero MI. Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population. Tropical Medicine and Infectious Disease. 2023; 8(10):473. https://doi.org/10.3390/tropicalmed8100473
Chicago/Turabian StyleGutierrez-Castañeda, Luz D., Carmen R. Acosta, Mónica A. Bustos, Diana K. García, Diana P. Bohada, Raúl Rodríguez, and Martha Inirida Guerrero. 2023. "Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population" Tropical Medicine and Infectious Disease 8, no. 10: 473. https://doi.org/10.3390/tropicalmed8100473
APA StyleGutierrez-Castañeda, L. D., Acosta, C. R., Bustos, M. A., García, D. K., Bohada, D. P., Rodríguez, R., & Guerrero, M. I. (2023). Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population. Tropical Medicine and Infectious Disease, 8(10), 473. https://doi.org/10.3390/tropicalmed8100473