| Literature DB >> 22457818 |
Amal Assaf1, Tong Van Hoang, Imad Faik, Toni Aebischer, Peter G Kremsner, Jürgen F J Kun, T P Velavan.
Abstract
BACKGROUND: Ficolin-2 coded by FCN2 gene is a soluble serum protein that plays an important role in innate immunity. In this study, we analyzed five functional polymorphisms of the FCN2 gene for their possible association with cutaneous leishmaniasis.Entities:
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Year: 2012 PMID: 22457818 PMCID: PMC3311577 DOI: 10.1371/journal.pone.0034113
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Primer pairs utilized for characterization of the entire FCN2 gene in 40 Syrian Arabs.
| Reverse primer | Forward primer | |
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| Promoter+Exon 1 |
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| Exon 2+3 |
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| Exon 4+6 |
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| Exon 5 | |
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| Exon 7+8 |
used only for sequencing.
Primers and probes employed for genotyping three promoter SNPs in the FCN2 gene.
| Position | Primer/Probe | Sequence |
| −986G>A | Primers |
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| Probes |
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| −602G>A | Primers |
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| Probes |
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| −4A>G | Primers |
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| Probes |
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YAK and FAM are the reporter fluorophores Yakima Yellow and Fluorescein, respectively.
Each probe carries at the 3′-end the dark BBQ (BlackBerry Quencher).
Characterization of the entire FCN2 gene in 40 Syrian Arabs.
| Base position | SNP rs#. | Major allele | Minor allele | Major allele | Minor allele |
| −986 | rs3124952 | G | A | 0. 50 | 0. 50 |
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| rs76739162 | C | T | 0. 99 | 0. 01 |
| −602 | rs3124953 | G | A | 0. 71 | 0. 29 |
| −557 | rs3811140 | A | G | 0. 73 | 0. 27 |
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| rs74693003 | G | A | 0. 99 | 0. 01 |
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| rs12344051 | G | A | 0. 97 | 0. 03 |
| −64 | rs28969369 | A | C | 0. 86 | 0. 14 |
| −4 | rs17514136 | A | G | 0. 81 | 0. 19 |
| 1878 | rs3124955 | T | C | 0. 62 | 0. 38 |
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| rs75577478 | G | C | 0. 97 | 0. 03 |
| 2051 | rs73565973 | T | C | 0. 90 | 0. 10 |
| 2088 | rs73565979 | C | T | 0. 90 | 0. 10 |
| 2182 | rs12344423 | G | A | 0. 51 | 0. 49 |
| 2417 | rs7024491 | A | G | 0. 66 | 0. 34 |
| 2472 | rs3128624 | A | G | 0. 63 | 0. 37 |
| 2488 | rs4520243 | T | C | 0. 62 | 0. 38 |
| 2545 | rs7037264 | G | A | 0. 63 | 0. 37 |
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| rs76665625 | C | G | 0. 99 | 0. 01 |
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| rs75123259 | C | T | 0. 99 | 0. 01 |
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| rs56117058 | G | C | 0. 86 | 0. 14 |
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| rs77254375 | G | A | 0. 99 | 0. 01 |
| 4888 | rs56200327 | C | T | 0. 99 | 0. 01 |
| 6031 | rs11103563 | A | G | 0. 97 | 0. 03 |
| 6183 | rs62573178 | G | A | 0. 92 | 0. 08 |
| 6220 | rs7872508 | T | G | 0. 97 | 0. 03 |
| 6359 | rs17549193 | C | T | 0. 81 | 0. 19 |
| 6424 | rs7851696 | G | T | 0. 97 | 0. 03 |
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| rs76267164 | G | A | 0. 99 | 0. 01 |
In bold = new SNPs.
Figure 1Haploview plot illustrating the linkage disequilibrium of the FCN2 promoter region from 40 healthy Syrian individuals.
At the top the SNPs are shown according to their succession from the start of translation of the FCN2 gene. Empty squares indicate a high degree of LD (LD coefficient D′ = 1) between pairs of markers. Numbers indicate the D′ value expressed as a percentile. Red squares indicate pairs in strong LD with LOD scores for LD ≥2; purple squares, D′ = 1 with LOD = 2; white squares, D′ <1.0 and LOD ≤2.
Figure 2Haploview plot illustrating the linkage disequilibrium of the FCN2 functional variants in controls (2A) and patients (2B).
At the top the SNPs are shown according to their succession from the start of translation of the FCN2 gene. Empty squares indicate a high degree of LD (LD coefficient D′ = 1) between pairs of markers. Numbers indicate the D′ value expressed as a percentile. Red squares indicate pairs in strong LD with LOD scores for LD ≥70; purple squares, D′ = 1 with LOD >1; white squares, D′ <1.0 and LOD ≤2.
FCN2 haplotypes in Cutaneous Leishmaniasis patients and healthy controls.
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| Patients n = 452 (%) | Healthy controls n = 572 (%) | OR (95% CI) |
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| AAACG | 79 (17.5) | 118 (20.6) | NS | |
| GGACG | 160 (35.4) | 206 (36.0) | NS | |
| AGGTG | 116 (25.7) | 136 (23.8) | NS | |
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| GGACT | 37 (8.2) | 46 (8.0) | NS | |
| AGGCG | 9 (2.0) | 3 (0.5) | NS | |
| GGATG | 6 (1.3) | 15 (2.6) | NS | |
| GGATT | 1 (0.2) | 6 (1.0) | NS | |
| AGATG | 0 | 3 (0.5) | NS | |
| AAATG | 1 (0.2) | 4 (0.7) | NS | |
| GGGTG | 0 | 3 (0.5) | NS | |
| AGGTT | 0 | 2 (0.3) | NS | |
| GAACG | 0 | 2 (0.3) | NS | |
| AAACT | 1 (0.2) | 0 | NS | |
Figure 3Distribution of serum ficolin levels to five major haplotypes (−986/−602/−4/+6359/+6424) in 70 control individuals.