Complete Linkage Disequilibrium Research Articles

Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses

BackgroundGreying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation.ResultsWe found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the ~350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present.ConclusionsThese results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.

Progesterone receptor variants associated with the PROGINS haplotype exhibit functional properties similar to those of wild-type progesterone receptor

The progesterone receptor (PR) is a ligand-activated transcription factor existing in two isoforms, A (PRA) and B (PRB), resulting from alternative promoter usage. It has long been speculated that genetic variants of PR are associated with the risk for various benign and malignant diseases, but data from clinical trials and in-vitro studies remain contradictory. The most extensively studied variant is termed PROGINS and consists of an intronic 320-bp Alu insertion and two coding (Ser344Thr, Val660Leu) and one silent single nucleotide polymorphism in complete linkage disequilibrium (allele frequency in Caucasians 9-19%). Our study aimed at elucidating the functional consequences of the PROGINS-associated single nucleotide polymorphisms of PRA and PRB (i.e. Thr344 and Leu660) as compared with wild-type PR (Ser344, Val660). The two PRA and two PRB full-length receptor variants were expressed by adenovirus in the PR-negative human breast cancer cell line T47D-Y and assayed with respect to transactivational properties, c-src activation, combined net mRNA and protein stability and hormone-binding characteristics. In all experiments the wild-type PR and the PROGINS variant were undistinguishable. Though there still might be tissue specific effects of the variants, our data indicate that these common PR variants do not functionally differ, which may provide a basis to explain the heterogeneous outcome of association studies.

Functional Differences Exist between TNFα Promoters Encoding the Common −237G SNP and the Rarer HLA-B*5701-Linked A Variant

A large body of functional and epidemiological evidence have previously illustrated the impact of specific MHC class I subtypes on clinical outcome during HIV-1 infection, and these observations have recently been re-iterated in genome wide association studies (GWAS). Yet because of the complexities surrounding GWAS-based approaches and the lack of knowledge relating to the identity of rarer single nucleotide polymorphism (SNP) variants, it has proved difficult to discover independent causal variants associated with favourable immune control. This is especially true of the candidate variants within the HLA region where many of the recently proposed disease influencing SNPs appear to reflect linkage with ‘protective’ MHC class I alleles. Yet causal MHC-linked SNPs may exist but remain overlooked owing to the complexities associated with their identification. Here we focus on the ancestral TNFα promoter −237A variant (rs361525), shown historically to be in complete linkage disequilibrium with the ‘protective’ HLA-B*5701 allele. Many of the ancestral SNPs within the extended TNFα promoter have been associated with both autoimmune conditions and disease outcomes, however, the direct role of these variants on TNFα expression remains controversial. Yet, because of the important role played by TNFα in HIV-1 infection, and given the proximity of the −237 SNP to the core promoter, its location within a putative repressor region previously characterized in mice, and its disruption of a methylation-susceptible CpG dinucleotide motif, we chose to carefully evaluate its impact on TNFα production. Using a variety of approaches we now demonstrate that carriage of the A SNP is associated with lower TNFα production, via a mechanism not readily explained by promoter methylation nor the binding of transcription factors or repressors. We propose that the −237A variant could represent a minor causal SNP that additionally contributes to the HLA-B*5701-mediated ‘protective’ effect during HIV-1 infection.

Association ofGNLYGenetic Polymorphisms with Chronic Liver Disease in a Korean Population

Granulysin (GNLY) is found in cytotoxic granules of cytolytic T lymphocytes and natural killer (NK) cells, which are critical for hepatitis B virus (HBV) clearance. GNLY cytotoxicity plays an important role in the defense against viruses or intracellular bacteria. We hypothesized that genetic variation in the GNLY gene could affect the resistance of hosts against HBV infection. We compared the distribution frequencies of GNLY polymorphisms between an HBV-induced chronic liver disease (CLD) group and a spontaneous recovery (SR) control group to determine whether GNLY polymorphisms play a role in HBV clearance. A total of 117 patients in the SR group and 230 patients in the CLD group were enrolled. Samples derived from complex infections, including hepatitis C and human immunodeficiency virus, and those associated with insufficient clinical information (10 samples in SR and 24 samples in CLD) were excluded from the study. The final analysis included 107 SR and 206 CLD samples. DNA was extracted from peripheral blood, and GNLY genotypes were determined by the GoldenGate(®) method. The genotype distribution of the single-nucleotide polymorphisms (SNPs) rs2886767 (C>T), rs1561285 (G>C), and rs11127 (T>C) were significantly different between the SR and CLD groups in a recessive model (p<0.015). These three SNPs were in a complete linkage disequilibrium (LD) block. Diplotype distributions of haplotype (HT) 1 (C-G-T) and HT2 (T-C-C) were significantly different between the SR and CLD groups in a recessive model (p=0.025) and a dominant model (p=0.008). All p-values remained significant after multiple comparisons. GNLY polymorphism genotypes and diplotypes were associated with the chronicity of HBV. These data suggested that genetic variation of GNLY may be an important factor in HBV clearance through the CD8+ T or NK cell-mediated removal of HBV-infected cells from the host.

Variation in the ovocalyxin‐32 gene in commercial egg‐laying chickens and its relationship with egg production and egg quality traits

Avian eggshell quality is an important trait for commercial egg production, as the eggshell is the primary packaging material and antimicrobial barrier for the internal food resource. Strong eggshells are essential to ensure that eggs can reach their final destination without damage. Ovocalyxin-32 (OCX32) is a matrix protein found within the outer layers of the eggshell and in the cuticle. Numerous reports in the literature have identified association between variants in the gene encoding this protein, OCX32, and various eggshell quality traits. Thus, OCX32 is a candidate gene for selection for eggshell traits in commercial poultry populations. Sequencing of exons 2-6 of the OCX32 gene in eight elite brown and white eggshell commercial egg-laying lines revealed 28 SNPs and one SNP/indel. Eighteen of these SNPs were predicted to alter the amino acid sequence of the protein. Clusters of SNPs in complete linkage disequilibrium were found in both exons 2 and 6. A total of 19 different versions or protein-sequence haplotypes of the OCX32 protein were inferred, revealing considerable variation within commercial lines. Genotypes for 13 of the SNPs were determined for 330-1819 individuals per line. Trait association studies revealed a significant effect of OCX32 on shell color in white egg lines and line-specific significant effects on albumen height, early egg weight, puncture score, and yolk weight. Three of the lines showed a significant change in OCX32 frequency over time, indicating selection pressure for certain variants of this gene during the breeding program.

Mutations in lipopolysaccharide-binding protein (LBP) gene change the susceptibility to clinical mastitis in Chinese Holstein

Mastitis is an unsolved human challenge all dairy farms facing with, which leads to immeasurable economic loss to the farmers. LBP gene plays a vital role in the innate immune recognition of Gram-negative bacterium that is a major cause of bovine clinical mastitis, but little is known about LBP mutations and their effects on cows' susceptibility to clinical mastitis. In this study, PCR-SSCP method was adopted to analyze SNPs of LBP gene in Chinese Holstein for the first time. 17 SNPs were found in the promoter core region, exon1, exon2, exon3, exon4 and exon8. The mutation g.-81C → T in promoter leads to an AP-2 binding site lost. Two mutations, g.11T → C (4 Leu → Ser) and g.68G → C (23Gly → Ala) in signal peptide brought about molecular secondary structural change, meanwhile, g.11T → C made a Big-1 domain lost, and there was an N-myristoylation site at the g.68G/C locus. The three mutations above were in complete linkage disequilibrium in allele A. In mature LBP protein, five mutations were found: g.3034G → A(36Asp → Asn), g.3040A → G(38Asn → Asp), g.3056T → C(43Ile → Thr) in allele D; g.4619G → A(67Ala → Thr) in allele F; 19975G → A (282Val → Met) in allele J. And SNPs in allele D and F were in complete linkage disequilibrium, also in which 38Asn → Asp and 67Ala → Thr influenced the protein secondary structure. Prediction of the 3-D structure shows mutations 36Asp → Asn, 38Asn → Asp and 43 Ile → Thr were on the concave surface of LBP protein at barrel-N, 67Ala → Thr was in the apolar pocket at barrel-N. Motif analysis shows 36Asp → Asn causes loss of a CK2 phosphorylation site, 67 Ala → Thr forms a new PKC phosphorylation site. And 43Ile → Thr, 67Ala → Thr made hydrophobic amino acids to be hydrophilic amino acids. Interestingly, the morbidity of AB (mixed type g.-81C/T, g.11T/C, g.68G/C), CD (mixed type g.3034G/A, g.3040A/G, g.3056T/C) and EF (mixed type g.4619G/A) genotype cows are significant higher than others in this study (P < 0.01), and it can be deduced that the SNPs in these 3 genotypes might affect the secretion of LBP protein and regulate the binding ability of LBP protein to LPS. Taken together, it is revealed that these SNPs may hold the secret of susceptibility to clinical mastitis in Chinese Holstein.

A Functional Variation in CD55 Increases the Severity of 2009 Pandemic H1N1 Influenza A Virus Infection

Infection due to 2009 pandemic H1N1 influenza A virus (A[H1N1]pdm09) is commonly manifested as mild infection but occasionally as severe pneumonia. We hypothesized that host genetic variations may contribute to disease severity. An initially small-scale genome-wide association study guided the selection of CD55 single-nucleotide polymorphisms in 425 Chinese patients with severe (n = 177) or mild (n = 248) disease. Carriers of rs2564978 genotype T/T were significantly associated with severe infection (odds ratio, 1.75; P = .011) under a recessive model, after adjustment for clinical confounders. An allele-specific effect on CD55 expression was revealed and ascribed to a promoter indel variation, which was in complete linkage disequilibrium with rs2564978. The promoter variant with deletion exhibited significantly lower transcriptional activity. We further demonstrated that CD55 can protect respiratory epithelial cells from complement attack. Additionally, A(H1N1)pdm09 infection promoted CD55 expression. In conclusion, CD55 polymorphisms are associated with severe A(H1N1)pdm09 infection. CD55 may exert a substantial impact on the disease severity of A(H1N1)pdm09 infection.

The Good SHP2 Association

In this issue of the Journal, Goodship and colleagues report results from an association study for common genetic variants underlying tetralogy of Fallot (TOF).1 By studying a limited number of single-nucleotide polymorphisms (SNPs) tagging haplotypes at 22 candidate genes, they associated a single SNP at a chromosome 12 locus harboring PTPN11 , which encodes the protein tyrosine phosphatase SHP2, and other genes with TOF. This SNP was calculated to have a per-allele risk of 1.34 and a population-attributable risk of roughly 5%. If this study, undertaken with British white subjects, can be replicated in additional populations, it will represent a significant advance in our understanding of the genetics of congenital heart defects (CHD). Article see p 287 The genetic architecture of CHD has been the source of considerable debate and uncertainty. It has been known for some time that chromosomal defects and single-gene mutations can cause CHD, often in the context of a multisystem disease. For TOF, examples include trisomy 21 and TBX5 point mutations underlying Down and Holt-Oram syndromes, respectively.2 The discovery of 22q11 microdeletions, usually arising de novo, added significantly to our understanding of the genetic underpinnings of conotruncal forms of CHD, as these account for substantial percentages of some cardiac lesions (eg, 34% of truncus arteriosus and 16% of TOF).3 Nonetheless, these known genetic causes of CHD are estimated to account for less than 20% of cases overall. Epidemiological studies of CHD have strongly pointed to genetic factors as the predominant cause, although environmental exposures are also relevant. Parental consanguinity significantly increases the risk of CHD in offspring, probably as the result of the shared genetic background of unaffected parents.4 In countries where consanguineous marriages are customary, the rates of consanguinity are 2- to 3-fold higher among couples with offspring with CHD than …

OC-010 Detailed analysis of ATG16L1 demonstrates gene-wide extent of association with crohn's disease susceptibility

IntroductionATG16L1 has been implicated in the susceptibility to Crohn's disease (CD), notably the T300A (rs2241880, exon 9). In ATG16L1-deficient and hypomorphic mice, autophagy, Paneth-cell homeostasis and IL-1b secretion were dependent...

IL28B Genetic Variation Is Associated with Spontaneous Clearance of Hepatitis C Virus, Treatment Response, Serum IL-28B Levels in Chinese Population

BackgroundThe interleukin-28B gene (IL28B) locus has been associated with host resistance to hepatitis C virus (HCV) infection and response to PEG-IFN/RBV treatment in western populations. This study was to determine whether this gene variant is also associated with spontaneous clearance of HCV infection, treatment response and IL-28B protein production in Chinese patients.MethodsWe genotyped IL28B genetic variations (rs12980275, rs8103142, rs8099917 and rs12979860) by pyrosequencing DNA samples from cohorts consisting of 529 subjects with persistent HCV infection, 196 subjects who cleared the infection, 171 healthy individuals and 235 chronic HCV patients underwent IFN/RBV treatment. The expression of IL-28B were measured by ELISA and RT-PCR.ResultsWe found that the four IL28B variants were in complete linkage disequilibrium (r2 = 0.97–0.98). The rs12979860 CC genotype was strongly associated with spontaneously HCV clearance and successful IFN/RBV treatment compared to the CT/TT. IL-28B levels in persistent HCV patients were significantly lower than subjects who spontaneously resolved HCV and healthy controls and were also associated with high levels of ALT (alanine aminotransferase) and AST (aspartate aminotransferase). IL-28B levels were also significantly lower in individuals carrying T alleles than CC homozygous.ConclusionsThus, the rs12979860-CC variant upstream of IL28B gene is associated with spontaneous clearance of HCV, susceptible to IFN/RBV treatment and increased IL-28B levels in this Chinese population.

Linear models for breeding values prediction in haplotype-assisted selection - an analysis of QTL-MAS Workshop 2011 Data

BackgroundThe aim of this study was to estimate haplotype effects and then to predict breeding values using linear models. The haplotype based analysis enables avoidance of loosing information due to linkage disequilibrium between single markers. There are also less explanatory variables in the linear model which makes the estimation more reliable.MethodsDifferent methods and criteria for marker and haplotype selection were considered. First, markers with MAF lower than 5% where excluded from the data set. Then, SNPs in complete linkage disequilibrium where selected. Next step was to construct haplotypes and to estimate their frequencies basing on selected SNPs. The haplotypes with a frequency lower than 1% were not considered in further analysis. Chosen haplotypes were used as the explanatory variables in the linear models for breeding values prediction. Linear models with fixed and random haplotype effects as well as animal model were tested.ResultsThe number of markers was limited to 1206, 1189, 1249, 1288 and 1167 for chromosome 1, 2, 3, 4 and 5, respectively due to MAF criterion. In total 409 subsets of SNPs with r2=1 were found. 1476 haplotypes with different lengths were inferred. The frequencies of 817 haplotypes were higher than 1% - 184 for the first chromosome, 172 for the second, 131 for the third, 146 for the forth and 184 haplotypes for the fifth chromosome. The haplotype effects estimated using random models were comparable and more precise in prediction for individuals with unknown phenotypes. A few haplotypes with large effects were found when their effects were defined as fixed in the linear model . The correlations of the predicted breeding values with true breeding values were not that high. This could be brought about by selection criteria imposed on the genotype data which led to substantial reduction of number of markers.ConclusionsAlthough not many markers were considered in the study, the results obtained show that the implemented approach can be considered as quite promising. The haplotype approach let to avoid high dimensional models as compared with single SNPs models.

Variations of the angiotensin II type 1 receptor gene are associated with extreme human longevity

Longevity phenotype in humans results from the influence of environmental and genetic factors. Few gene polymorphisms have been identified so far with a modest effect on lifespan leaving room for the search of other players in the longevity game. It has been recently demonstrated that targeted disruption of the mouse homolog of the human angiotensin II type 1 receptor (AT1R) gene (AGTR1) translates into marked prolongation of animal lifespan (Benigni et al., J Clin Invest 119(3):524-530, 2009). Based on the above study in mice, here we sought to search for AGTR1 variations associated to reduced AT1 receptor protein levels and to prolonged lifespan in humans. AGTR1 was sequenced in 173 Italian centenarians and 376 younger controls. A novel non-synonymous mutation was detected in a centenarian. Two polymorphisms in AGTR1 promoter, rs422858 and rs275653, in complete linkage disequilibrium, were significantly associated with the ability to attain extreme old age. We then replicated the study of rs275653 in a large independent cohort of Japanese origin (598 centenarians and semi-supercentenarians, 422 younger controls) and indeed confirmed its association with exceptional old age. In combined analyses, rs275653 was associated to extreme longevity either at recessive model (P = 0.007, odds ratio (OR) 3.57) or at genotype level (P = 0.015). Significance was maintained after correcting for confounding factors. Fluorescence activated cell sorting analysis revealed that subjects homozygous for the minor allele of rs275653 had less AT1R-positive peripheral blood polymorphonuclear cells. Moreover, rs275653 was associated to lower blood pressure in centenarians. These findings highlight the role of AGTR1 as a possible candidate among longevity-enabling genes.

MDM2 Promoter SNP344T&gt;A (rs1196333) Status Does Not Affect Cancer Risk

The MDM2 proto-oncogene plays a key role in central cellular processes like growth control and apoptosis, and the gene locus is frequently amplified in sarcomas. Two polymorphisms located in the MDM2 promoter P2 have been shown to affect cancer risk. One of these polymorphisms (SNP309T>G; rs2279744) facilitates Sp1 transcription factor binding to the promoter and is associated with increased cancer risk. In contrast, SNP285G>C (rs117039649), located 24 bp upstream of rs2279744, and in complete linkage disequilibrium with the SNP309G allele, reduces Sp1 recruitment and lowers cancer risk. Thus, fine tuning of MDM2 expression has proven to be of significant importance with respect to tumorigenesis. We assessed the potential functional effects of a third MDM2 promoter P2 polymorphism (SNP344T>A; rs1196333) located on the SNP309T allele. While in silico analyses indicated SNP344A to modulate TFAP2A, SPIB and AP1 transcription factor binding, we found no effect of SNP344 status on MDM2 expression levels. Assessing the frequency of SNP344A in healthy Caucasians (n = 2,954) and patients suffering from ovarian (n = 1,927), breast (n = 1,271), endometrial (n = 895) or prostatic cancer (n = 641), we detected no significant difference in the distribution of this polymorphism between any of these cancer forms and healthy controls (6.1% in healthy controls, and 4.9%, 5.0%, 5.4% and 7.2% in the cancer groups, respectively). In conclusion, our findings provide no evidence indicating that SNP344A may affect MDM2 transcription or cancer risk.

Association between a variant of the sigma-1 receptor gene and Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with complex etiology and strong genetic predisposition. A number of investigations support the possible involvement of sigma non-opioid intracellular receptor 1 (SIGMAR1) in the pathophysiology of AD. We aimed to investigate the association between SIGMAR1 polymorphisms and late-onset AD, therefore we genotyped rs1799729 (GC-241-240TT) and rs1800866 (Q2P) in 322 Hungarian late-onset AD patients and 250 ethnically matched, elderly control individuals. The investigated polymorphisms were in nearly complete linkage disequilibrium resulting in the GC-Q and TT-P predominant haplotypes that were subjected to the statistical analyses. Our data demonstrates an association between the SIGMAR1 TT-P variant and the risk for developing AD (p=0.019), and a potential modest interaction effect (p=0.058) of the co-presence of the TT-P haplotype with apolipoprotein E4 allele on the risk for AD. Based on this mild significance, we could not fully support the hypothesis that TT-P haplotype in interaction with APOE E4 allele confers risk for developing AD.

97 Detailed Analysis of ATG16L1 Demonstrates Gene-Wide Extent of Association With Crohn's Disease Susceptibility

Introduction ATG16L1 has been implicated in the susceptibility to Crohn9s disease (CD), notably the T300A (rs2241880, exon 9). In ATG16L1-deficient and hypomorphic mice, autophagy, Paneth-cell homeostasis and IL-1b secretion were dependent on ATG16L1 (Saitoh et al Nature 2008, Cadwell et al Cell 2010). In contrast, studies focusing on T300A have shown conflicting results (Kuballa et al PLoS ONE 2008, Fujita et al JBC 2009). The association at other susceptibility loci (eg, NOD2 and IL23R) consists of common and rare variants (Rivas et al Nat Genet 2011). Exon-sequencing studies have not demonstrated rare variants within the 18 exons of ATG16L1. Our aim was to analyse the ATG16L1 association signal, specifically focusing on common variants. Methods 38 single nucleotide polymorphisms (SNPs) spanning the ATG16L1 gene were imputed for 1735 subjects (800 CD/935 controls) (Franke et al Nat Genet 2010). Single SNP and haplotype frequency (>1%, solid spine of Linkage disequilibrium (LD), D’>0.8) association and permutation (n=10 000) analyses were performed (Haploview). Logistic regression (using SNPs p 0.8, between CD and controls. Results Single SNP permutation analysis yielded association of 16 markers (p 2 characteristics, showed 12 SNPs were in complete LD with rs2241880 (D9 and r 2 0.98−1). rs6758317 (r 2 =0.25, intron 2), rs3792106 (r 2 =0.76, intron 11), rs4663396 (r 2 =0.25, intron 12) and rs1045100 (r 2 =0.84) demonstrated strong association, independent of rs2241880. Regression analysis retained rs3792106, rs6754677 (intron 14) and rs1045100 (39UTR) (p −5 . Conclusion We demonstrated that the rs2241880 alone is not sufficient to explain the strong ATG16L1 association. Additional variants, independent of rs2241880, could implicate any of the coiled-coil domain, the WD domain and/or the 39 UTR, in CD susceptibility. Competing interests None declared.

Peptidylarginine Deiminase Type 4 and Methyl-CpG Binding Domain 4 Polymorphisms in Chinese Patients with Rheumatoid Arthritis

Peptidylarginine deiminase type 4 (PADI4) and methyl-CpG binding domain 4 (MBD4) are closely related with rheumatoid arthritis (RA). We hypothesized that PADI4 and MBD4 polymorphisms may contribute to RA susceptibility. We studied PADI4 rs2240340 G/A, PADI4 rs874881 C/G, MBD4 rs140693 G/A, and MBD4 rs2005618 T/C gene polymorphisms in 329 patients with RA and 697 controls in a Chinese population. Genotyping was done using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). When the PADI4 rs2240340 GG homozygote genotype was used as the reference group, the AA genotype was associated with a significantly increased risk of RA. In the recessive model, when PADI4 rs2240340 GG/GA genotypes were used as the reference group, the AA homozygote genotype was associated with a significant increased susceptibility to RA. PADI4 rs874881 C/G was in complete linkage disequilibrium with PADI4 rs2240340 G/A. MBD4 rs140693 G/A and MBD4 rs2005618 T/C polymorphisms were not associated with the risk of RA. In stratification analyses, a significantly increased risk for RA associated with the PADI4 rs2240340 AA genotype was evident among older patients and patients who were anticitrullinated protein antibody (ACPA)-positive compared with the PADI4 rs2240340 GG/GA genotype. These findings suggest that the functional single-nucleotide polymorphism PADI4 rs2240340 G/A variant allele is associated with RA development, especially among older patients and ACPA-positive patients. However, our results were obtained from a moderate-sized sample, and therefore this is a preliminary conclusion. Validation by a larger study from a more diverse ethnic population is needed to confirm these findings.

A functional variant in the promoter region regulates the C‐reactive protein gene and is a potential candidate for increased risk of atrial fibrillation

In a large population-based cohort, the level of C-reactive protein (CRP) in patients at baseline predicts an increased risk of future development of atrial fibrillation (AF). The mechanism of this increased risk is unknown. Furthermore, both the molecular effects of CRP on atrial myocytes and fibroblasts and whether genetic variants in the CRP gene predispose to AF are also unknown. A genetic association study between CRP gene polymorphisms and AF was performed in two independent populations (I: 100 AF patients and 101 controls; II: 348 AF patients and 356 controls), with functional studies to elucidate the mechanism of association. Three polymorphisms (T-861C, A-821G and C-390A/C-390T) were found in the 1-kb promoter of CRP. A triallelic polymorphism (C-390A/C-390T) captured all haplotype information and determined the CRP gene promoter activity and the plasma CRP level, and was in nearly complete linkage disequilibrium with G1059C polymorphism in exon 2. The -390A variant was associated with a higher CRP gene promoter activity, a higher plasma CRP level and a higher risk of AF. Patients with AF also had a higher plasma CRP level than controls. CRP significantly increased the inward L-type calcium current in atrial myocytes with no changes in other ionic currents. CRP did not affect the expressions of type I alpha 1 (COL1A1), type III alpha 1 (COL3A1) and type 1 alpha 2 (COL1A2) procollagens in atrial fibroblasts. A CRP gene promoter triallelic polymorphism was associated with CRP gene promoter activity, determined the plasma level of CRP, and predicted the risk of AF. The mechanism of this may be via augmention of calcium influx by CRP in atrial myocytes, but not because of atrial fibrosis.

Associations between interleukin-10 polymorphisms and susceptibility to psoriasis: a meta-analysis

The aim of this study was to determine whether three specific interleukin-10 (IL-10) polymorphisms confer susceptibility to psoriasis. A meta-analysis was conducted on the associations between the IL-10-1082 G/A, -592 C/A polymorphisms and haplotypes of the IL-10-1082 G/A, -592 C/A, -819 C/T polymorphisms and psoriasis. A total of eight studies involving 1,018 psoriasis patients and 1,186 controls were considered in the meta-analysis. No association was found between psoriasis and the IL-10-1082 G allele in all study subjects [odds ratio (OR)=1.098, 95% confidence interval (CI)=0.923-1.306, p=0.291] or between this allele and psoriasis in Europeans (OR=0.990, 95% CI=0.809-1.214, p=0.925), but a significant association was found in Asians (OR=1.785, 95% CI=1.144-2.76, p=0.011). Three polymorphisms at the promoter region of IL-10 (-1082 G/A, -819 C/T, -592 C/A) are known to be in complete linkage disequilibrium, but no association was found between the haplotype and psoriasis. This meta-analysis shows that the IL-10-1082 G/A polymorphism confers susceptibility to psoriasis in Asians, and suggests that the IL-10 promoter -1082 polymorphism has an ethnicity-specific effect.

Potential Association Between Frequent Nonsynonymous Variant of NPPA and Cardioembolic Stroke

Atrial natriuretic peptide (ANP, also known as NPPA) and brain natriuretic peptide (BNP, also known as NPPB) have been determined as genetic factors for several diseases, including stroke and myocardial infarction, in human and rat models. To investigate the potential association between polymorphisms of the NPPA gene and stroke in a Korean population, nine single-nucleotide polymorphisms (SNPs) of NPPA and NPPB genes were genotyped in a total of 941 Korean subjects, including 674 stroke patients (109 hemorrhagic and 565 ischemic) and 267 unaffected controls. Genotype comparisons of the targeted alleles revealed that there were no significant associations between stroke patients and control subjects, or among hemorrhagic, ischemic, and control groups. However, in logistic analysis for Trial of Org 10172 in Acute Stroke Treatment (TOAST) classification of ischemic stroke, nonsynonymous rs5065 (STOP152Arg) and rs5067 in 3'UTR of NPPA, which were in complete linkage disequilibrium, showed significant associations with cardioembolic stroke. These two SNPs showed higher frequencies in cardioembolic stroke patients than those in controls and ischemic patients with small-vessel occlusion (p=0.002, adjusted p=0.02). It was also found that NPPA rs5065C allele in all of the Korean subjects existed as heterozygous compared with Caucasian and African populations. Although further replications in larger cardioembolic stroke subjects are required, our preliminary findings suggest that the nonsynonymous rs5065C of the NPPA gene, which could produce a new or dysfunctional transcript, is possibly associated with cardioembolism.

Genetic variants in SCN5A promoter are associated with arrhythmia phenotype severity in patients with heterozygous loss-of-function mutation

Heterozygous SCN5A mutations have been associated with varied arrhythmia phenotypes; phenotype severity may range from asymptomatic electrocardiographic changes (mild phenotype) to symptomatic arrhythmias resulting in syncope, cardiac arrest, and sudden cardiac death (severe phenotype) even among family members carrying the same mutation. Risk-stratification schemes for SCN5A mutation carriers remain uncertain. To determine the role of SCN5A promoter variants and DNA methylation by using a family-based approach in predicting phenotype severity in a kindred with loss-of-function SCN5A mutation. In a large kindred with a heterozygous SCN5A loss-of-function mutation (1936delC, Q646RfsX5; 22 mutation carriers), we sought SCN5A promoter variants. In addition, we assessed SCN5A and genome-wide DNA methylation profiles on genomic DNA derived from blood (Illumina Human Methylation27 BeadChip). During systematic survey of the 2.8-kb SCN5A promoter region, we identified 2 single nucleotide polymorphisms in complete linkage disequilibrium (rs41310749 and rs41310239). These promoter variants were significantly associated with disease severity (mild vs severe phenotype) (P = .0007), as all 3 patients with severe phenotype carried the 2-SNP variant on both mutant and wild-type alleles. Analysis did not support a role for the methylation of SCN5A-related genes. These family-based genetic findings suggest that the presence of specific promoter variants increase the risk of a severe phenotype in heterozygous carriers of an SCN5A loss-of-function mutation.