A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility

Kochi, Yuta; Okada, Yukinori; Suzuki, Akari; Ikari, Katsunori; Terao, Chikashi; Takahashi, Atsushi; Yamazaki, Keiko; Hosono, Naoya; Myouzen, Keiko; Tsunoda, Tatsuhiko; Kamatani, Naoyuki; Furuichi, Tatsuya; Ikegawa, Shiro; Ohmura, Koichiro; Mimori, Tsuneyo; Matsuda, Fumihiko; Iwamoto, Takuji; Momohara, Shigeki; Yamanaka, Hisashi; Yamada, Ryo; Kubo, Michiaki; Nakamura, Yusuke; Yamamoto, Kazuhiko

doi:10.1038/ng.583

Cited by 245 publications

(203 citation statements)

References 41 publications

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“…Even when a significant association of a variant was observed in multiple populations, the effect sizes and allele frequencies would not be identical between the populations. 90 Most of the recent studies have used metaanalysis assuming a fixed-effect model for effect sizes; however, metaanalysis assuming a random-effect model or other sophisticated methods is required for trans-ethnic studies. 91,92 Prioritization of GWAS results using external biological databases To effectively explore the genetic loci that were uncaptured by the standard GWAS approach, it would be important to assess the subloci of GWAS results by prioritizing or weighting them by incorporating information from external biological databases (Figure 2b).…”

Section: Meta-analysis Of Gwas Involving Multiple Populationsmentioning

confidence: 99%

Common genetic factors for hematological traits in Humans

Okada

Kamatani

2012

J Hum Genet

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Section: Meta-analysis Of Gwas Involving Multiple Populationsmentioning

confidence: 99%

Common genetic factors for hematological traits in Humans

Okada

Kamatani

2012

J Hum Genet

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“…Moreover, mutations in CCR6 are also known to be responsible for other autoinflammatory disorders. For instance, the polymorphism rs3093024 in CCR6 associated with susceptibility to rheumatoid arthritis was observed in Japanese population (Kochi et al, 2010). Our case-control study, we finally found that T allele, TC/TT genotypes can significantly reduce susceptibility to digestive disorders in rabbit.…”

Section: Resultsmentioning

confidence: 57%

The polymorphism and gene expression of chemokine receptor 6is associated with digestive disorders in rabbits

Zhong

Chen

et al. 2016

IJAR

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This study aimed to investigate the possible involvement of Chemokine receptor 6 (CCR6) gene in genetic susceptibility to digestive disorders in rabbits. A total of 346 samples (161 cases vs 185 controls) were used for this case-control association study. One coding SNP (c.96C>T) spanning the CCR6 gene coding region was identified by direct sequencing and then genotyped using PCR-SSCP. The results revealed that individuals with allele "T" was significantly protective against digestive disorders (odds ratio=0.66, 95% confidence interval: 0.46-0.94, P<0.05), and TC/TT genotype can significantly reduce the incidence of digestive disorders (odds ratio=0.64, 95% CI: 0.41-0.99, P<0.05). we also investigated CCR6 gene mRNA expression level in different severity status of digestive disorders. The significantly higher mRNA expression level of sacculus rotundus in severe group was observed compared with mild and health group (P<0.05), in addition, the individuals with CC genotype had a higher mRNA expression than TC and TT genotype (P<0.05).

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“…RA, in fact, responds to the definition of 'complex genetic disease'. A recent meta-analysis [78] conducted on Europeans has shown how complex the disease is by adding to the known susceptibility genes, 7 more, one of which is also shared by the Asian population [79]. These results have helped better characterize RA in the European and Asian population.…”

Section: A Case Study: Application To Immune Diseasesmentioning

confidence: 99%

Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures

Yang

Wei

Tang

et al. 2013

Sci. China Life Sci.

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Microarray and deep sequencing technologies have provided unprecedented opportunities for mapping genome mutations, RNA transcripts, transcription factor binding, and histone modifications at high resolution at the genome-wide level. This has revolutionized the way in which transcriptomes, regulatory networks and epigenetic regulations have been studied and large amounts of heterogeneous data have been generated. Although efforts are being made to integrate these datasets unbiasedly and efficiently, how best to do this still remains a challenge. Here we review major impacts of high-throughput genome-wide data generation, their relevance to human diseases, and various bioinformatics approaches for data integration. Finally, we provide a case study on inflammatory diseases. genomics, epigenomics, phenomics, integration, data analysis Citation:Yang L, Wei G, Tang K, et al. Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures. Sci China Life Sci, 2013Sci, , 56: 213 -219, doi: 10.1007 Twelve years ago, the unveiling of the first human reference genome sequence [1,2] inspired researchers to believe that genome-based discoveries would revolutionize the study and clinical treatment of human diseases. As genome sequences from different individuals became available, comparative genomics using computational approaches emerged as a powerful method for understanding gene functions at the genome-wide level. These approaches unveiled more variations between individuals than were initially expected [3]. Genomic variations (including single nucleotide polymorphism (SNPs) and insertions and deletions (indels)) responsible for some of hereditary diseases have been identified and applied to examine genomes of thousands of individuals for correlations between the presence of variants and traits of interests [4]. First microarrays were used, then exon sequencing, and now whole genome sequencing has become a popular tool [5,6]. Currently, many variations from numerous sites in the genome have been successfully connected with different human diseases including various types of cancers [6] using DNA sequencing technology which underwent a 14000-fold drop in cost between 1999 and 2009 [7], and computational imputation methods [8].Though most studies have focused on the connection between genomic variations (both common and rare) and human diseases, mechanisms underlying many of the DNA variations have not been clearly addressed. Genome information alone is not sufficient to interpret complex diseases [9]. Evidence at epigenome, post-transcriptome, and even the human microbiome levels is beginning to shed new light on human disease-related studies beyond the genome level.

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A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility

Cited by 245 publications

References 41 publications

Common genetic factors for hematological traits in Humans

Common genetic factors for hematological traits in Humans

The polymorphism and gene expression of chemokine receptor 6is associated with digestive disorders in rabbits

Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures

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