Psoriasis is a complex genetic disease, which has previously been associated with numerous single nucleotide polymorphisms (SNPs) that are implicated in various processes, including skin barrier functions and in the regulation of inflammatory and immune responses. The present study aimed to investigate the genotypic and allelic frequencies of 32 SNPs at 24 genetic loci, and their association with psoriasis in a Mexican population. These SNPs, which were associated with psoriasis in previous studies, included the following genes: Major histocompatibility complex class I-C (
Psoriasis is a multisystem chronic inflammatory disease, which affects ~2% of the worldwide population (
Due to the relatively high heritability of psoriasis, genetic analyses, including linkage and/or association studies, have been conducted worldwide in order to identify genes that may affect the risk of developing psoriasis (
Various single nucleotide polymorphisms (SNPs) have previously been associated with an increased risk of developing psoriasis. These SNPs are involved in various processes, including: Skin barrier functions [late cornified envelope (
Previous studies investigating the association between SNPs and psoriasis have predominantly analyzed European, American, and Asian populations (
The present study (register no. DE11-004) was conducted at the Department of Genetics, University Hospital ‘Dr. José Eleuterio González’ (Monterrey, México), with approval from the Committee for Ethics, Research and Biosecurity of the School of Medicine, University Hospital ‘Dr. José Eleuterio González’, Autonomous University of Nuevo León.
Written informed consent was obtained from all the patients enrolled, following an explanation of the nature of the study. A total of 46 patients (32 males and 14 females; age, 26–72 years), who had been diagnosed with chronic plaque psoriasis, were recruited from the Dermatology Outpatient Clinic at the University Hospital ‘Dr. José Eleuterio González’ between November 2011 and May 2012. Patients diagnosed with other clinical subtypes of psoriasis or other genetic diseases, as well as affected relatives of the patients in the study, were excluded.
A total of 103 peripheral blood samples (from 56 males and 47 females; age, 26–72 years) from control subjects without psoriasis (age, 26–72 years) were obtained from the DNA Bank of the Department of Genetics at the University Hospital ‘Dr. José Eleuterio González’.
A total of 32 SNPs from 24 genes and 2 intergenic regions, which were previously associated with psoriasis in various populations, were selected. The SNPs included in the study were associated with the following genes:
Molecular analyses were conducted using the TaqMan® assay (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA), and were analyzed using the OpenArray® NT Genotyping system (Applied Biosystems; Thermo Fisher Scientific, Inc.). DNA was extracted from 200 µL EDTA-treated whole blood samples, using the QIAamp Blood Mini kit on the automated QIAcube system (Qiagen, Hilden, Germany). Purified DNA was collected in a final volume of 150 µL and stored at −20°C until use. DNA for OpenArray (OA) analysis was diluted at a concentration of 50 ng/µl and a ratio of A260/280 and A260/230 of 1.6–1.9. A non-template control, which consisted of DNase-free double-distilled water, was used in each plate assay. The DNA sample (50 ng/µl) and TaqMan OpenArray Master Mix (Applied Biosystems; Thermo Fisher Scientific, Inc.) were mixed in a 384-well plate, and transferred to the OA plate using an autoloader, after which the OA plate was filled with immersion fluid and sealed with glue. Multiplex TaqMan® assay reactions were carried out in a Dual Flat Block GeneAmp PCR system 9700 (Applied Biosystems; Thermo Fisher Scientific, Inc.), and the PCR cycling conditions were as follows: An initial step at 93°C for 10 min; followed by 50 cycles at 95°C for 45 sec, 94°C for 13 sec and 53°C for 2 min, 14 sec; followed by a final step at 25°C for 2 min. The samples were maintained at 4°C until further use. The plate was designed to analyze 32 TaqMan® assays for each sample. The allele analysis was conducted using the TaqMan® Genotyper Software 1.0, with the default parameters, according to the manufacturer's protocol (Applied Biosystems; Thermo Fisher Scientific, Inc.). The accuracy of the genotyping was assessed by comparisons with 15 samples, which had been genotyped three times, resulting in 45 comparison per SNP.
Genetic analyses were conducted using the Golden Helix SNP & Variation Suite 7.6 program (Golden Helix, Inc., Bozeman, MT, USA). The 32 SNPs were analyzed for deviation from the Hardy-Weinberg equilibrium using the Fisher's exact test (P<0.01 was considered to indicate a statistically significant difference). An association study was performed using the Basic Allelic test and Fisher's exact test in order to assess ORs, 95% confidence intervals (CIs) and P-values. In addition, Bonferroni P-values and false discovery rates (FDR) were calculated in order to exclude spurious associations. P≤0.05/32 SNPs (1.56×10−3) was considered to indicate a statistically significant difference.
The genetic analysis included samples from 46 patients and 103 controls (age range, 26–72 years). Of the patients, 32 were male (69.56%) and 14 were female (30.43%), of which 6 patients (13.04%) had a family history of psoriasis. A total of 17 patients (36.95%) had mild, 25 patients (54.34%) had moderate, and 2 patients (4.34%) presented severe psoriasis. Articular and nail involvement were detected in 4 (8.69%) and 18 (39.13%) patients respectively.
Genotype frequencies of the 32 SNPs in both groups are presented in
Of the 32 SNPs, six were shown to confer risk for psoriasis, including:
In the present study, six SNPs corresponding to different genes were associated with an increased risk of developing psoriasis, of which the
The
The rs1265181 SNP of the
The rs6125829 SNP of the
The rs3212227 and rs3213094 SNPs of the
The
The present study demonstrated that the allele frequencies of
To the best of our knowledge, the present study is the first to investigate the association between genetic regions that have previously been associated with psoriasis in other populations, including Asian and European populations, and psoriasis in the Mexican Mestizo population. The results of the present study suggested that SNPs in the
In conclusion, the present study observed that in Mexican patients with plaque psoriasis, SNPs from different genes associated with immune response or membrane cell repair confer an increased risk for disease development.
SNPs analyzed in patients with psoriasis and controls.
Fisher's Exact | Allele Freq. | Fisher's HWE P | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene/SNP | SNP | Chr | P | Bonf. P | FDR | OR (95% CI) | Cases | Controls | Cases | Controls |
rs10484554 | 6 | 0.003 | 0.100 | 0.100 | T 3.51 (1.54–7.99) | 0.167 | 0.054 | 0.582 | 1.000 | |
C 0.28 (0.13–0.65) | 0.833 | 0.946 | ||||||||
rs1265181 | 6 | 0.010 | 0.326 | 0.163 | C 2.83 (1.29–6.23) | 0.163 | 0.064 | 0.009 | 0.003 | |
G 0.35 (0.16–0.78) | 0.837 | 0.936 | ||||||||
rs6125829 | 20 | 0.014 | 0.444 | 0.148 | T 0.51 (0.30–0.86) | 0.318 | 0.480 | 0.489 | 0.070 | |
G 1.98 (1.17–3.35) | 0.682 | 0.520 | ||||||||
rs3213094 | 5 | 0.018 | 0.569 | 0.142 | T 0.51 (0.30–0.89) | 0.267 | 0.414 | 0.701 | 0.100 | |
C 1.94 (1.13–3.36) | 0.733 | 0.586 | ||||||||
rs3212227 | 5 | 0.025 | 0.805 | 0.161 | G 0.53 (0.31–0.92) | 0.267 | 0.406 | 0.701 | 0.408 | |
T 1.88 (1.09–3.24) | 0.733 | 0.594 | ||||||||
rs6887695 | 5 | 0.269 | 1.000 | 0.614 | C 0.72 (0.41–1.27) | 0.239 | 0.304 | 0.698 | 0.484 | |
G 1.39 (0.79–2.44) | 0.761 | 0.696 | ||||||||
rs17728338 | 5 | 0.055 | 1.000 | 0.293 | A 2.41 (1.00–5.77) | 0.120 | 0.053 | 0.103 | 0.245 | |
G 0.42 (0.17 −0.99) | 0.880 | 0.947 | ||||||||
rs512625 | 20 | 0.078 | 1.000 | 0.356 | A 1.75 (0.96–3.19) | 0.250 | 0.160 | 1.000 | 0.284 | |
G 0.57 (0.31–1.04) | 0.750 | 0.840 | ||||||||
rs597980 | 20 | 0.609 | 1.000 | 0.974 | G 1.18 (0.71–1.94) | 0.489 | 0.448 | 1.000 | 0.067 | |
A 0.85 (0.52–1.40) | 0.511 | 0.552 | ||||||||
rs677044 | 20 | 0.524 | 1.000 | 0.931 | G 1.27 (0.69–2.33) | 0.217 | 0.180 | 0.661 | 0.736 | |
A 0.79 (0.43–1.45) | 0.783 | 0.820 | ||||||||
rs361525 | 6 | 0.084 | 1.000 | 0.337 | A 2.08 (0.95–4.58) | 0.144 | 0.075 | 0.206 | 0.433 | |
G 0.48 (0.22–1.06) | 0.856 | 0.925 | ||||||||
rs1800629 | 6 | 0.097 | 1.000 | 0.346 | A 2.20 (0.93–5.18) | 0.120 | 0.058 | 0.103 | 1.000 | |
G 0.46 (0.19–1.07) | 0.880 | 0.942 | ||||||||
rs1799964 | 6 | 0.642 | 1.000 | 0.978 | C 0.84 (0.45–1.57) | 0.185 | 0.213 | 1.000 | 0.039 | |
T 1.19 (0.64–2.23) | 0.815 | 0.787 | ||||||||
rs20541 | 5 | 0.103 | 1.000 | 0.329 | G 1.55 (0.94–2.54) | 0.565 | 0.456 | 0.227 | 0.003 | |
A 0.65 (0.39–1.06) | 0.435 | 0.544 | ||||||||
rs8016947 | 14 | 0.155 | 1.000 | 0.451 | T 0.64 (0.36–1.15) | 0.207 | 0.289 | 0.659 | 0.095 | |
G 1.56 (0.87–2.82) | 0.793 | 0.711 | ||||||||
rs2903908 | 20 | 0.222 | 1.000 | 0.592 | C 0.62 (0.29–1.31) | 0.109 | 0.165 | 1.000 | 1.000 | |
T 1.62 (0.76–3.44) | 0.891 | 0.835 | ||||||||
rs4795067 | 17 | 0.267 | 1.000 | 0.657 | G 1.39 (0.82–2.37) | 0.337 | 0.267 | 1.000 | 0.799 | |
A 0.72 (0.42–1.22) | 0.663 | 0.733 | ||||||||
rs6908425 | 6 | 0.286 | 1.000 | 0.610 | T 0.68 (0.36–1.28) | 0.174 | 0.235 | 0.601 | 0.788 | |
C 1.46 (0.78–2.74) | 0.826 | 0.765 | ||||||||
rs4649203 | 1 | 0.287 | 1.000 | 0.574 | G 0.56 (0.22–1.44) | 0.065 | 0.110 | 1.000 | 1.000 | |
A 1.77 (0.69–4.53) | 0.935 | 0.890 | ||||||||
rs4112788 | 1 | 0.523 | 1.000 | 0.984 | A 1.21 (0.74–1.99) | 0.435 | 0.388 | 0.382 | 0.305 | |
G 0.83 (0.50–1.36) | 0.565 | 0.612 | ||||||||
rs17716942 | 2 | 0.597 | 1.000 | 1.000 | C 0.67 (0.21–2.11) | 0.043 | 0.064 | 1.000 | 1.000 | |
T 1.50 (0.47–4.72) | 0.957 | 0.936 | ||||||||
rs2066808 | 12 | 0.651 | 1.000 | 0.948 | G 1.29 (0.55–3.03) | 0.098 | 0.078 | 0.351 | 1.000 | |
A 0.78 (0.33–1.83) | 0.902 | 0.922 | ||||||||
rs7799039 | 7 | 0.702 | 1.000 | 0.977 | A 1.11 (0.67–1.83) | 0.413 | 0.388 | 0.225 | 0.678 | |
G 0.90 (0.55–1.49) | 0.587 | 0.612 | ||||||||
rs610604 | 6 | 0.705 | 1.000 | 0.940 | G 0.89 (0.54–1.46) | 0.413 | 0.442 | 0.225 | 1.000 | |
T 1.12 (0.68–1.85) | 0.587 | 0.558 | ||||||||
rs6809854 | 3 | 0.779 | 1.000 | 0.997 | G 0.91 (0.52–1.60) | 0.267 | 0.285 | 0.245 | 0.806 | |
- |
A 1.10 (0.63–1.92) | 0.733 | 0.715 | |||||||
rs7574865 | 2 | 0.800 | 1.000 | 0.984 | T 1.10 (0.67–1.80) | 0.435 | 0.413 | 0.227 | 0.546 | |
G 0.91 (0.56–1.50) | 0.565 | 0.587 | ||||||||
rs240993 | 6 | 0.800 | 1.000 | 0.948 | C 0.91 (0.55–1.49) | 0.413 | 0.437 | 0.545 | 0.228 | |
T 1.10 (0.67–1.81) | 0.587 | 0.563 | ||||||||
rs7530511 | 1 | 0.858 | 1.000 | 0.980 | T 0.92 (0.44–1.89) | 0.130 | 0.141 | 0.561 | 0.414 | |
C 1.09 (0.53–2.25) | 0.870 | 0.859 | ||||||||
rs702873 | 2 | 0.887 | 1.000 | 0.978 | T 0.92 (0.52–1.61) | 0.250 | 0.267 | 0.242 | 0.449 | |
C 1.09 (0.62–1.92) | 0.750 | 0.733 | ||||||||
rs27524 | 5 | 0.887 | 1.000 | 0.946 | A 0.94 (0.53–1.65) | 0.250 | 0.262 | 0.430 | 0.071 | |
G 1.07 (0.61–1.88) | 0.750 | 0.738 | ||||||||
rs12924903 | 16 | 1.000 | 1.000 | 1.000 | A 0.98 (0.59–1.63) | 0.380 | 0.385 | 0.032 | 0.529 | |
G 1.02 (0.61–1.69) | 0.620 | 0.615 | ||||||||
rs4810485 | 20 | 1.000 | 1.000 | 1.000 | T 1.03 (0.56–1.90) | 0.207 | 0.201 | 1.000 | 1.000 | |
G 0.97 (0.53–1.78) | 0.793 | 0.799 |
P<0.05 indicates a statistically significant difference. CI, confidence interval; OR, odds ratio; SNP, single nucleotide polymorphism; P, P-value; Bonf. Bonferroni correction; FDR, false discovery rate; HWE, Hardy-Weinberg Equilibrium; Chr, chromosome;