Junghyun Namkung

IL-5 and IL-5 receptor alpha polymorphisms are associated with atopic dermatitis in Koreans

Background:  Eosinophils are recruited into the affected tissue of asthma and atopic dermatitis (AD) patients. IL‐5 and IL‐5R are highly expressed in the AD skin lesions, yet the reported levels of IL‐8 are controversial.

New evaluation measures for multifactor dimensionality reduction classifiers in gene–gene interaction analysis

MOTIVATION Gene-gene interactions are important contributors to complex biological traits. Multifactor dimensionality reduction (MDR) is a method to analyze gene-gene interactions and has been applied to many genetics studies of complex diseases. In order to identify the best interaction model associated with disease susceptibility, MDR classifiers corresponding to interaction models has been constructed and evaluated as a predictor of disease status via a certain measure such as balanced accuracy (BA). It has been shown that the performance of MDR tends to depend on the choice of the evaluation measures. RESULTS In this article, we introduce two types of new evaluation measures. First, we develop weighted BA (wBA) that utilizes the quantitative information on the effect size of each multi-locus genotype on a trait. Second, we employ ordinal association measures to assess the performance of MDR classifiers. Simulation studies were conducted to compare the proposed measures with BA, a current measure. Our results showed that the wBA and tau(b) improved the power of MDR in detecting gene-gene interactions. Noticeably, the power increment was higher when data contains the greater number of genetic markers. Finally, we applied the proposed evaluation measures to real data.

An association between IL-9 and IL-9 receptor gene polymorphisms and atopic dermatitis in a Korean population

BACKGROUND The genes encoding IL-9 and IL-9R have recently been implicated in the genetic basis of asthma and allergy. Although studies performed on transgenic and knockout mice have shown conflicting results, no evidence of skin changes has ever been reported in these animals. OBJECTIVE To find association of the SNPs in IL-9 and IL-9R genes and interaction of these genes in atopic dermatitis. METHOD We genotyped 5 SNPs from the IL-9 and IL-9R genes of 1090 subject samples (631 AD patients and 459 normal controls). A luciferase assay was then performed for the rs31563 (-4091G/A) SNP located in the IL-9 gene promoter region. RESULT The rs31563 (-4091G/A) SNP in the IL-9 gene was significantly associated with the AD phenotype, especially allergic-type AD. In the luciferase assay, the rs31563 G construct was observed to have 1.54 times higher activity than the rs31563 A construct. Although no association was found between SNPs in IL-9R gene and AD, the rs3093467 SNP showed association with non-allergic AD. In the gene-gene interaction analysis, we found that IL-9/IL-9R genotype rs31563 GG/rs3093467 TT conveyed a greater risk for AD phenotype development. CONCLUSION Significant evidence exists to suggest that the rs31563 SNP (-4091G/A) located in the IL-9 gene is associated with an increased susceptibility to AD. Similarly, the rs3093467 SNP in IL-9R gene seems to be associated with an increased risk for developing non-allergic AD. In a subsequent gene-gene interaction analysis, the rs31563 GG/rs3093467 TT genotype combination (IL-9/IL-9R) was found to exert a synergistic effect in the development of the AD phenotype. As the classes of helper T cells are diverse and the function of IL-9 cytokine has not been fully described, the cutaneous function of IL-9 needs to be further explored in future studies.

Association of single nucleotide polymorphisms in the IL-12 (IL-12A and B) and IL-12 receptor (IL-12Rβ1 and β2) genes and gene-gene interactions with atopic dermatitis in Koreans.

BACKGROUND The acute skin lesions of atopic dermatitis (AD) are associated with Th2 cells; however, the chronic skin lesions of AD are associated with Th1 cells via the action of IL-12. OBJECTIVE We evaluated the associations of single nucleotide polymorphisms (SNPs) and haplotype in the IL-12 and IL-12 receptor genes, and determined the gene-gene interactions between the SNPs of these genes and the SNPs of the IL-18 gene that we previously reported. METHOD We genotyped 24 SNPs from 4 IL-12/IL-12R genes for 1089 case-control samples (631 AD patients and 458 normal controls). We measured the serum IL-12 concentrations in 89 individuals (79 AD patients and 10 controls) by ELISA. We analyzed the SNPs and haplotypes in each gene and also searched for the gene-gene interactions. RESULT The rs582504 (IVS-798A/T) SNP and the haplotype TA (rs582054 and rs2243151) in the IL-12A gene, and the rs438421 (IVS12+1266T/C) SNP and the haplotype CCA (rs375947, rs438421, and rs1870063) in the IL-12RB1 gene were significantly associated with the AD phenotype. We showed that the rs438421 polymorphism in the IL-12RB1 (TT) gene and the rs2066446 polymorphism in the IL-12RB2 (AA) gene had a significant interaction to develop the ADe phenotype (allergic type of AD), and those individuals with the risk alleles, TT/AA/CC (IL-12RB1/IL-12RB2/IL-18), have more than a 10-fold increased risk to develop ADe. CONCLUSION This study provides evidence for a significant interaction between the IL-12RB1 and IL-12RB2 genes that contribute to a 4-fold increased risk for developing ADe. In addition to the IL-12R interaction, we suggest that the IL-18 gene can significantly interact with the IL-12R gene to develop ADe. In addition to the interaction, the SNPs and haplotypes in the IL-12A and IL-12RB1 genes are independently and significantly associated with the AD phenotype, and especially with the ADe phenotype. This data may contribute to our understanding of AD genetic interactions and account for the additional risk of certain patients to develop AD.

Single nucleotide polymorphisms and the haplotype in the DEFB1 gene are associated with atopic dermatitis in a Korean population

BACKGROUND Atopic dermatitis (AD) patients have been recognized to have an increased susceptibility to cutaneous colonization and infection by bacteria, fungi and viruses. OBJECTIVE We wanted to evaluate the associations of single nucleotide polymorphism (SNP) and the haplotype in the defensin (DEFA) and defensin (DEFB) genes, and so we performed genotyping for the SNPs in these genes in both AD patients and normal controls. METHOD We genotyped 27 SNPs from the DEFA 4, 5 and 6 genes and the DEFB1 gene for 1089 case-control samples (631 AD patients and 458 normal controls). We analyzed the SNPs and haplotypes in each gene. RESULT We identified that two SNPs and the haplotype CT in the DEFB1 gene are associated with AD in Koreans. The rs5743399 (-2266T/C) SNP is associated with AD, and especially with the high IgE, extrinsic type, and the rs5743409 (-1241T/G) SNP is associated with AD. On the haplotype analysis of these two SNPs, the haplotype CT is associated with AD, and especially with the allergic, extrinsic type of AD. However, we could not find any significant associations between the SNPs in the three DEFA genes and AD. CONCLUSION We found that the rs5743399 SNP, the rs5743409 SNP and the CT haplotype in the DEFB1 gene were significantly associated with the susceptibility to AD. We also found that rs5743399 polymorphism and the haplotype CT in this gene showed a strong association with the allergic, extrinsic type of AD. These results suggest that the DEFB1 gene has a main effect on the skin inflammation and/or skin responsiveness to any kind of allergic reaction.

Association of polymorphisms in genes encoding IL‐4, IL‐13 and their receptors with atopic dermatitis in a Korean population

Abstract:  Th2‐dominated immune responses are believed to contribute to the pathogenesis of atopic dermatitis (AD). IL‐4 and IL‐13 are typical pleiotropic Th2 cytokines that play a central role in IgE‐dependent inflammatory reactions. Single‐nucleotide polymorphisms (SNPs) in IL‐4 and IL‐13 have been reported in patients with allergic disease from numerous countries. Gene–gene interactions among genes have been identified in patients with asthma, although negative results have been reported. To investigate the associations of SNPs in these genes and the interactions between these genes in AD, we genotyped 23 SNPs of the IL‐4, IL‐13, IL‐4R, IL‐13Rα1 and IL‐13Rα2 genes for 1089 case‐control samples (631 AD patients and 458 controls) and analysed the SNPs and haplotypes in these genes. We also searched for gene–gene interactions among these five genes. Our data identified an association between rs3091307 and rs20541 in the IL‐13 gene and between rs2265753 and rs2254672 in the IL‐13Rα1 gene and the AD phenotype. In particular, three of the four SNPs were especially predictive of the allergic type of AD (ADe), and the haplotype TCGG in the IL‐13Rα1 gene showed significant association with AD, especially ADe. Furthermore, the combination of rs3091307 GG/ rs2265753 GG (IL‐13/IL‐13Rα1) conveyed a significantly higher risk for developing ADe. However, we did not identify any SNPs in the IL‐4, IL‐4R and IL‐13Rα2 genes that were associated with AD. As IL‐13Rα1 is most likely expressed in Th17 cells rather than in Th2 cells, these data suggest diversity in the classification of Th cells that needs to be verified in future studies.

Noninvasive Prenatal Diagnosis of Duchenne Muscular Dystrophy: Comprehensive Genetic Diagnosis in Carrier, Proband, and Fetus

BACKGROUND Noninvasive prenatal diagnosis of monogenic disorders using maternal plasma and targeted massively parallel sequencing is being investigated actively. We previously demonstrated that comprehensive genetic diagnosis of a Duchenne muscular dystrophy (DMD) patient is feasible using a single targeted sequencing platform. Here we demonstrate the applicability of this approach to carrier detection and noninvasive prenatal diagnosis. METHODS Custom solution-based target enrichment was designed to cover the entire dystrophin (DMD) gene region. Targeted massively parallel sequencing was performed using genomic DNA from 4 mother and proband pairs to test whether carrier status could be detected reliably. Maternal plasma DNA at varying gestational weeks was collected from the same families and sequenced using the same targeted platform to predict the inheritance of the DMD mutation by their fetus. Overrepresentation of an inherited allele was determined by comparing the allele fraction of 2 phased haplotypes after examining and correcting for the recombination event. RESULTS The carrier status of deletion/duplication and point mutations was detected reliably through using a single targeted massively parallel sequencing platform. Whether the fetus had inherited the DMD mutation was predicted correctly in all 4 families as early as 6 weeks and 5 days of gestation. In one of these, detection of the recombination event and reconstruction of the phased haplotype produced a correct diagnosis. CONCLUSIONS Noninvasive prenatal diagnosis of DMD is feasible using a single targeted massively parallel sequencing platform with tiling design.

Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method.

Gene‐gene interaction is believed to play an important role in understanding complex traits. Multifactor dimensionality reduction (MDR) was proposed by Ritchie et al. [2001. Am J Hum Genet 69:138–147] to identify multiple loci that simultaneously affect disease susceptibility. Although the MDR method has been widely used to detect gene‐gene interactions, few studies have been reported on MDR analysis when there are missing data. Currently, there are four approaches available in MDR analysis to handle missing data. The first approach uses only complete observations that have no missing data, which can cause a severe loss of data. The second approach is to treat missing values as an additional genotype category, but interpretation of the results may then be not clear and the conclusions may be misleading. Furthermore, it performs poorly when the missing rates are unbalanced between the case and control groups. The third approach is a simple imputation method that imputes missing genotypes as the most frequent genotype, which may also produce biased results. The fourth approach, Available, uses all data available for the given loci to increase power. In any real data analysis, it is not clear which MDR approach one should use when there are missing data. In this article, we consider a new EM Impute approach to handle missing data more appropriately. Through simulation studies, we compared the performance of the proposed EM Impute approach with the current approaches. Our results showed that Available and EM Impute approaches perform better than the three other current approaches in terms of power and precision. Genet. Epidemiol. 33:646–656, 2009.

Capability of common SNPs to tag rare variants

Genome-wide association studies are based on the linkage disequilibrium pattern between common tagging single-nucleotide polymorphisms (SNPs) (i.e., SNPs having only common alleles) and true causal variants, and association studies with rare SNP alleles aim to detect rare causal variants. To better understand and explain the findings from both types of studies and to provide clues to improve the power of an association study with only common SNPs genotyped, we study the correlation between common SNPs and the presence of rare alleles within a region in the genome and look at the capability of common SNPs in strong linkage disequilibrium with each other to capture single rare alleles. Our results indicate that common SNPs can, to some extent, tag the presence of rare alleles and that including SNPs in strong linkage disequilibrium with each other among the tagging SNPs helps to detect rare alleles.

Hint for association of single nucleotide polymorphisms and haplotype in SPINK5 gene with atopic dermatitis in Koreans.

Abstract:  Clinical studies, including twin studies, support the concept that the risk of atopic dermatitis (AD) may be mediated through skin‐specific genes, rather than simply through systemic immune or atopy risk genes. The SPINK5 gene is expressed on epithelial surfaces and may provide protection against other allergenic serine proteases. Mutations in the SPINK5 gene result in Netherton syndrome, a disorder characterised by AD, ichthyosis, and elevated serum IgE levels. We genotyped 21 single nucleotide polymorphisms (SNPs) from the SPINK5 gene for 1090 case–control samples (631 patients with AD and 459 normal controls) and analysed the SNPs and haplotypes in this gene and also searched for gene–gene interactions between SPINK5 and the DEFB1 gene that we previously reported. Six SNPs [rs17718511 (P = 0.026), rs17860502 (P = 0.024), KN0001820 (P = 0.045), rs60978485 (P = 0.007), rs17718737 (P = 0.02), and rs1422985 (P = 0.038)] and the haplotype TAA (rs60978485, rs6892205, rs2303064; P = 0.023) in the SPINK5 gene showed significant different allelic or genotypic distributions between the AD group and the control group. We also found that four SNPs [rs17718511 (P = 0.033), rs17860502 (P = 0.031), rs60978485 (P = 0.005), rs17718737 (P = 0.023)] and the haplotype TAA (P = 0.02) in the SPINK5 gene showed associations with the susceptibility of the allergic type of AD (ADe). In addition to this finding, we speculate that the SNPs from DEFB1 and SPINK5 affect the individual susceptibility to development of ADe in an additive manner. This study provides evidence for a significant interaction between allergens and the SPINK5 gene that may contribute to ADe susceptibility.