| Literature DB >> 24751681 |
Ruo-Xi Chen1, Wen-Min Lu1, Lu-Ping Zhu1, Mei-Ping Lu1, Mei-Lin Wang2, Yun-Li Wang1, Xin-Yuan Chen1, Xin-Jie Zhu1, Min Yin3, Zheng-Dong Zhang2, Lei Cheng3.
Abstract
BACKGROUND: The ADAM33 gene has been identified as a potentially important asthma candidate gene and polymorphisms in this gene have been shown to be associated with asthma and seasonal allergic rhinitis.Entities:
Mesh:
Substances:
Year: 2014 PMID: 24751681 PMCID: PMC3994017 DOI: 10.1371/journal.pone.0095033
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Primers and probes for genotypes screening by TaqMan allelic discrimination.
| NCBI rs No. | Base change | Primers | Probes |
| rs3918392 | A>G | F: | G allele: FAM-CCTGGAAAGGAGCCT-MGB |
| R: | A allele: HEX-CCTGGAAAGGAACC-MGB | ||
| rs528557 | C>G | F: | G allele: FAM-TGCTCCCAGGGGC-MGB |
| R: | C allele: HEX-TGCTCCCAGGCGC-MGB | ||
| rs2280091 | A>G | F: | C allele: FAM-CACCCCACGGAGTT-MGB |
| R: | T allele: HEX- ACCCCATGGAGTTGG-MGB | ||
| rs2280090 | A>G | F: | C allele: FAM-TGGACAGCCCTGGC-MGB |
| R: | T allele: HEX-TGGACAGTCCTGGC-MGB | ||
| rs3918400 | C>T | F: | T allele: FAM-AGTGGAGCTTTGACC-MGB |
| R: | C allele: HEX-TGGAGCTTCGACCC-MGB | ||
| rs2787094 | C>G | F: | C allele: FAM-CTCCCCTGCAGCCT-MGB |
| R: | G allele: HEX-CTCCCCTGGAGCCT-MGB | ||
| rs2787093 | C>T | F: | A allele: FAM-AGCCTAGATGGCAGC-MGB |
| R: | G allele: HEX-CCGAGCCTAGGTGG-MGB |
*The alleles were arrayed as the location of the primers or probes from 5′to 3′.
Distribution of selected variables among cases and controls.
| Variables | Cases ( | Controls ( |
| ||
| N | % | N | % | ||
| Age (years), mean ± SD | 19.68±12.6 | 20.10±12.61 | 0.597 | ||
| Sex | |||||
| Male | 342 | 66.4 | 299 | 60.4 | 0.086 |
| Female | 173 | 33.6 | 196 | 39.6 | |
| Serum total IgE (kU/L), median (IQR) | 265.0 (120.2–573.0) | 26.8 (11.1–52.2) | <0.001 | ||
| Eosinophil cationic protein (µg/L), median (IQR) | 14.3 (5.6–30.1) | 4.8 (3.1–7.5) | <0.001 | ||
| Duration of rhinitis (years), mean ± SD | 6.62±5.87 | ||||
| Total nasal symptoms (VAS score), mean ± SD | 5.23±2.41 | ||||
| Concomitant asthma | |||||
| Yes | 130 | 30.1 | |||
| No | 304 | 70.0 | |||
| Family history of allergic diseases | |||||
| Yes | 306 | 70.2 | |||
| No | 130 | 29.8 | |||
| Specific IgE (kUA/L), median (IQR) | |||||
|
| 27.4 (5.0–69.4) | ||||
|
| 23.1 (5.0–63.3) | ||||
*Derived from two-sided χ2 test for comparison of discrete variables and unpaired Student’s t-test for continuous variables.
Selective variables were transformed into logarithmic model before unpaired Student’s t-test between cases and controls.
Some information of concomitant asthma or family history of allergic diseases was not available in cases.
IQR, interquartile range; VAS, visual analogue scales.
Primary information of seven genotyped SNPs in the ADAM33 gene.
| SNPNo. | NCBIrs No. | Chromosomeposition | SNP namein ref. | Location | Base | MAF |
| Genotyped(%) | ||
| change | Database | Case | Control | |||||||
| 1 | rs3918392 | 3655219 | F1 | exon | A>G | 0.067 | 0.119 | 0.077 | 0.175 | 98.6 |
| 2 | rs528557 | 3651742 | S2 | exon | C>G | 0.250 | 0.266 | 0.206 | 0.916 | 98.3 |
| 3 | rs2280091 | 3650234 | T1 | exon | A>G | 0.078 | 0.093 | 0.072 | 0.782 | 96.6 |
| 4 | rs2280090 | 3650205 | T2 | exon | G>A | 0.100 | 0.109 | 0.102 | 0.332 | 98.1 |
| 5 | rs3918400 | 3649463 | V2 | 3′-UTR | C>T | 0.159 | 0.188 | 0.163 | 0.300 | 99.1 |
| 6 | rs2787094 | 3649161 | V4 | 3′-UTR | C>G | 0.410 | 0.563 | 0.547 | 0.251 | 99.1 |
| 7 | rs2787093 | 3648462 | 3′near gene | T>C | 0.233 | 0.282 | 0.226 | 0.145 | 98.0 | |
*SNP position in NCBI dbSNP (http://www.ncbi.nlm.nih.gov/snp).
MAF for CHB from the HapMap databases (http://www.hapmap.org) or NCBI dbSNP (http://www.ncbi.nlm.nih.gov/snp).
HWE P value in the control group.
SNP, single nucleotide polymorphism; MAF, minor allele frequencies; HWE, Hardy-Weinberg equilibrium; CHB: Han Chinese in Beijing, China.
Genotype and allele frequencies in ADAM33 polymorphisms among cases and controls.
| SNPNo. | NCBIrs No. | Genotypes | Cases | Controls | Crude OR | Adjusted OR |
| ||
| N | % | N | % | (95% CI) | (95% CI) | ||||
| 1 | rs3918392 |
|
| ||||||
| AA | 405 | 79.9 | 419 | 85.7 | 1.00 (reference) | 1.00 (reference) |
| ||
| AG | 83 | 16.4 | 65 | 13.3 | 1.32 (0.93–1.88) | 1.34 (0.94–1.91) | |||
| GG | 19 | 3.8 | 5 | 1.0 |
|
| |||
| AG/GG | 102 | 20.1 | 70 | 14.3 |
|
|
| ||
| G allele | 0.119 | 0.077 |
| ||||||
| 2 | rs528557 |
|
| ||||||
| CC | 288 | 56.7 | 306 | 63.1 | 1.00 (reference) | 1.00 (reference) |
| ||
| CG | 170 | 33.5 | 158 | 32.6 | 1.14 (0.87–1.50) | 1.15 (0.88–1.51) | |||
| GG | 50 | 9.8 | 21 | 4.3 |
|
| |||
| CG/GG | 220 | 43.3 | 179 | 36.9 |
|
|
| ||
| G allele | 0.266 | 0.206 |
| ||||||
| 3 | rs2280091 |
|
| ||||||
| AA | 416 | 81.9 | 403 | 86.1 | 1.00 (reference) | 1.00 (reference) | 0.190 | ||
| AG | 90 | 17.7 | 63 | 13.5 | 1.38 (0.98–1.96) | 1.38 (0.97–1.96) | |||
| GG | 2 | 3.9 | 2 | 4.3 | 0.97 (0.14–6.91) | 0.91 (0.13–6.49) | |||
| AG/GG | 91 | 17.9 | 64 | 13.7 | 1.38 (0.97–1.95) | 1.37 (0.97–1.94) | 0.073 | ||
| G allele | 0.093 | 0.072 | 0.093 | ||||||
| 4 | rs2280090 |
|
| ||||||
| GG | 406 | 80.4 | 394 | 81.1 | 1.00 (reference) | 1.00 (reference) | 0.685 | ||
| GA | 88 | 17.4 | 85 | 17.5 | 1.01 (0.72–1.40) | 1.00 (0.72–1.40) | |||
| AA | 11 | 2.2 | 7 | 1.4 | 1.53 (0.59–3.97) | 1.57 (0.60–4.10) | |||
| GA/AA | 99 | 19.6 | 92 | 18.9 | 1.04 (0.76–1.43) | 1.05 (0.76–1.43) | 0.788 | ||
| A allele | 0.109 | 0.102 | 0.609 | ||||||
| 5 | rs3918400 |
|
| ||||||
| CC | 337 | 66.3 | 342 | 69.4 | 1.00 (reference) | 1.00 (reference) | 0.175 | ||
| CT | 151 | 29.7 | 141 | 28.6 | 1.09 (0.83–1.43) | 1.07 (0.81–1.40) | |||
| TT | 20 | 3.9 | 10 | 2 | 2.03 (0.94–4.40) | 2.07 (0.95–4.50) | |||
| CT/TT | 171 | 33.7 | 151 | 30.6 | 1.15 (0.88–1.50) | 1.13 (0.87–1.48) | 0.305 | ||
| T allele | 0.188 | 0.163 | 0.147 | ||||||
| 6 | rs2787094 |
|
| ||||||
| CC | 87 | 17.1 | 95 | 19.3 | 1.00 (reference) | 1.00 (reference) | 0.674 | ||
| CG | 270 | 53.2 | 257 | 52.1 | 1.15 (0.82–1.61) | 1.14 (0.81–1.60) | |||
| GG | 151 | 29.7 | 141 | 28.6 | 1.17 (0.81–1.69) | 1.18 (0.81–1.71) | |||
| CG/GG | 421 | 82.9 | 398 | 80.7 | 1.16 (0.84–1.59) | 1.15 (0.84–1.59) | 0.379 | ||
| G allele | 0.563 | 0.547 | 0.462 | ||||||
| 7 | rs2787093 |
|
| ||||||
| TT | 259 | 51.2 | 284 | 58.8 | 1.00 (reference) | 1.00 (reference) |
| ||
| CT | 209 | 41.3 | 180 | 37.3 | 1.27 (0.98–1.65) | 1.29 (0.99–1.67) | |||
| CC | 38 | 7.5 | 19 | 3.9 |
|
| |||
| CT/CC | 247 | 48.8 | 199 | 41.2 |
|
|
| ||
| C allele | 0.282 | 0.226 |
| ||||||
*Adjusted for age and sex in logistic regression model.
Two-sided χ2 test for the distributions of genotype and allele frequencies.
Assumed risk alleles.
SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval.
Genotype frequencies of ADAM33 polymorphisms in dominant model in PER patients with and without asthma.
| SNPNo. | NCBIrs No. | Case with asthma | Case without asthma | ||
| Adjusted OR (95% CI) |
| Adjusted OR (95% CI) |
| ||
| 1 | rs3918392 | 1.28 (0.83–2.00) | 0.258 |
|
|
| 2 | rs528557 |
|
|
|
|
| 3 | rs2280091 |
|
| 1.35 (0.93–1.95) | 0.118 |
| 4 | rs2280090 | 1.24 (0.83–1.85) | 0.297 | 1.06 (0.75–1.49) | 0.748 |
| 5 | rs3918400 | 1.00 (0.70–1.42) | 1.000 | 1.12 (0.84–1.50) | 0.426 |
| 6 | rs2787094 | 1.48 (0.94–2.23) | 0.090 | 1.04 (0.74–1.47) | 0.818 |
| 7 | rs2787093 | 1.24 (0.89–1.72) | 0.208 |
|
|
Dominant model: MW+MM/WW; MW: heterozygotes; MM: mutation homozygotes; WW: wild homozygotes.
*Adjusted for age and sex in logistic regression model.
Two-sided χ2 test for the distributions of genotype frequencies.
PER, persistent allergic rhinitis; SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval.
Distributions of the ADAM33 combined genotypes among cases and controls.
| No. variant (risk) alleles ofthe combined alleles | Cases ( | Controls ( |
| ||
| N | % | N | % | ||
| 0 | 117 | 23.5 | 135 | 28.9 |
|
| 1 | 186 | 37.4 | 218 | 46.6 | |
| 2 | 125 | 25.5 | 92 | 19.7 | |
| 3 | 57 | 11.5 | 21 | 4.5 | |
| 4 | 12 | 2.4 | 2 | 0.4 | |
| Dichotomized groups | |||||
| 0–1 | 303 | 61.0 | 353 | 75.4 |
|
| 2–4 | 194 | 39.0 | 115 | 24.6 | |
*The number represents the numbers of risk genotypes.
Two-sided χ2 test for the distributions of combined genotype frequencies.
Association and stratification analyses between the ADAM33 combined genotypes and risk of PER.
| Variables | Subcategory | N (case/control) | Combined genotypes (case/control) | Adjusted OR(95% CI) | |||
| 0–1 | 2–4 | ||||||
| N | % | N | % | ||||
| Total | 497/468 | 303/353 | 61.0/75.4 | 194/115 | 39.0/24.6 |
| |
| Age (years) | |||||||
| <18 | 288/230 | 180/171 | 62.5/74.4 | 108/59 | 37.5/25.7 |
| |
| ≥18 | 209/238 | 123/182 | 58.9/76.5 | 86/56 | 41.2/23.5 |
| |
| Sex | |||||||
| Male | 329/292 | 207/221 | 62.9/75.7 | 122/71 | 37.1/24.3 |
| |
| Female | 168/176 | 96/132 | 57.1/75.0 | 72/44 | 42.9/25.0 |
| |
| Concomitant asthma | |||||||
| No | 294/468 | 188/353 | 63.9/75.4 | 106/115 | 36.1/24.6 | 1.00 (reference) | |
| Yes | 126/468 | 78/353 | 61.9/75.4 | 48/115 | 38.1/24.6 | 0.92 (0.59–1.42) | |
| Family history of allergic diseases | |||||||
| No | 293/468 | 188/353 | 64.2/75.4 | 105/115 | 35.8/24.6 | 1.00 (reference) | |
| Yes | 129/468 | 79/353 | 61.2/75.4 | 50/115 | 38.8/24.6 | 0.87 (0.56–1.36) | |
| VAS score | |||||||
| ≤5 | 277/468 | 162/353 | 58.5/75.4 | 115/115 | 41.5/24.6 | 1.00 (reference) | |
| >5 | 220/468 | 141/353 | 64.1/75.4 | 79/115 | 35.9/24.6 | 1.34 (0.92–1.94) | |
| Total IgE | |||||||
| Lower level | 403/468 | 237/353 | 58.8/75.4 | 166/115 | 41.2/24.6 | 1.00 (reference) | |
| Higher level | 94/468 | 66/353 | 70.2/75.4 | 28/115 | 29.8/24.6 | 1.14 (0.72–1.82) | |
*The number represents the numbers of risk genotypes.
Adjusted for age and sex in logistic regression model.
Lower level: below the 90th percentile of logarithmic total IgE; Higher level: above the 90th percentile of logarithmic total IgE.
PER, persistent allergic rhinitis; VAS, visual analogue scale; OR, odds ratio; CI, confidence interval.
Figure 1Linkage disequilibrium of seven SNPs in the ADAM33 gene.
Linkage disequilibrium (LD) of 7 SNPs was determined using the solid spine of LD option of Haploview 4.1. D′ values are displayed in the squares. Empty red squares have a pairwise D′ of 1.00. Red squares indicate high pairwise LD, gradually coloring down to white squares of low pairwise LD.
Associations between risk of PER and frequencies of inferred haplotypes on the basis of the observed genotypes among cases and controls.
| Haplotypes | Haplotype frequencies |
| Adjusted OR (95% CI) | |
| Cases | Controls | |||
| A-C-A-G-C-G-T | 0.291 | 0.312 | 0.3161 | 1.00 (reference) |
| A-C-A-G-C-C-C | 0.209 | 0.191 | 0.3305 | 1.17 (0.90–1.52) |
| A-C-A-G-C-C-T | 0.102 | 0.162 |
|
|
| A-G-A-G-T-G-T | 0.054 | 0.059 | 0.6011 | 0.99 (0.65–1.49) |
| A-C-A-G-C-G-C | 0.025 | 0.019 | 0.4246 | 1.35 (0.72–2.55) |
| A-G-G-A-C-G-T | 0.035 | 0.037 | 0.8596 | 1.02 (0.62–1.70) |
| A-G-A-G-C-G-T | 0.033 | 0.017 |
|
|
| A-G-A-G-C-C-T | 0.027 | 0.024 | 0.6621 | 1.21 (0.67–2.18) |
| A-C-A-G-T-G-T | 0.016 | 0.017 | 0.7647 | 0.95 (0.46–1.96) |
*The alleles of haplotypes were arrayed as the location of the SNPs in ADAM33 from 5′to 3′.
Two-sided χ2 test for each haplotype vs. all others combined in cases and controls.
Adjusted for age and sex in logistic regression model.
PER, persistent allergic rhinitis; OR, odds ratio; CI, confidence interval.