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31 papers found.
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Genome-Wide Association Study Confirming a Strong Effect of HLA and Identifying Variants in CSAD/lnc-ITGB7-1 on Chromosome 12q13.13 Associated With Susceptibility to Fulminant Type 1 Diabetes

The first genome-wide association study of fulminant type 1 diabetes was performed in Japanese individuals. As previously reported using a candidate gene approach, a strong association was observed with multiple single nucleotide polymorphisms (SNPs) in the HLA region, and the strongest association was observed with rs9268853 in the class II DR region ( P = 1.56 × 10−23, odds...

Increased expression and altered localization of cathepsin Z are associated with progression to jaundice stage in primary biliary cholangitis

• PubMed • Google Scholar Search for Yuki Hitomi in:Nature Research journals • PubMed • Google Scholar Search for Nao Nishida in:Nature Research journals • PubMed • Google Scholar Search for Minae

Interactions between cancer cells and normal cells via miRNAs in extracellular vesicles

Nao Nishida-Aoki 0 Takahiro Ochiya 0 0 N. Nishida-Aoki T. Ochiya (&) Division of Molecular and Cellular Medicine, National Cancer Center Research Institute , 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045

Genome-wide association study identified new susceptible genetic variants in HLA class I region for hepatitis B virus-related hepatocellular carcinoma

Nishida 10 11 17 Seik-Soon Khor 10 17 Masao Honda 12 17 Masaya Sugiyama 11 17 Natsumi 17 KayokoYamada 10 17 Norie Sawada 13 17 Shoichiro Tsugane 17 Kazuhiko Koike 13 14 17 Yuji Kondo 14 17 HiroshiYatsuhashi

Evolutionary Analysis of Classical HLA Class I and II Genes Suggests That Recent Positive Selection Acted on DPB1*04∶01 in Japanese Population

The human leukocyte antigen (HLA) genes exhibit the highest degree of polymorphism in the human genome. This high degree of variation at classical HLA class I and class II loci has been maintained by balancing selection for a long evolutionary time. However, little is known about recent positive selection acting on specific HLA alleles in a local population. To detect the...

No Evidence for Strong Recent Positive Selection Favoring the 7 Repeat Allele of VNTR in the DRD4 Gene

The human dopamine receptor D4 (DRD4) gene contains a 48-bp variable number of tandem repeat (VNTR) in exon 3, encoding the third intracellular loop of this dopamine receptor. The DRD4 7R allele, which seems to have a single origin, is commonly observed in various human populations and the nucleotide diversity of the DRD4 7R haplotype at the DRD4 locus is reduced compared to the...

Highly Parallel and Short-Acting Amplification with Locus-Specific Primers to Detect Single Nucleotide Polymorphisms by the DigiTag2 Assay

The DigiTag2 assay enables analysis of a set of 96 SNPs using Kapa 2GFast HotStart DNA polymerase with a new protocol that has a total running time of about 7 hours, which is 6 hours shorter than the previous protocol. Quality parameters (conversion rate, call rate, reproducibility and concordance) were at the same levels as when genotype calls were acquired using the previous...

Genome-Wide Association Study Identifies ZNF354C Variants Associated with Depression from Interferon-Based Therapy for Chronic Hepatitis C

The therapeutic use of interferon (IFN) is known to cause depression that frequently interrupts treatment. To identify genetic variants associated with IFN-induced depression, we conducted a genome-wide association study (GWAS) of 224 Japanese chronic hepatitis C patients receiving IFN-based therapy in a multicenter prospective study and stratified them into two groups according...

Comparative analysis of copy number variation detection methods and database construction

Background Array-based detection of copy number variations (CNVs) is widely used for identifying disease-specific genetic variations. However, the accuracy of CNV detection is not sufficient and results differ depending on the detection programs used and their parameters. In this study, we evaluated five widely used CNV detection programs, Birdsuite (mainly consisting of the...

Correction: A Genome-Wide Association Study for Diabetic Retinopathy in a Japanese Population: Potential Association with a Long Intergenic Non-Coding RNA

, Susumu Kurihara, Tomoko Morita-Ohkubo, Yumi Miyashita, Shigehiro Katayama, Keisuke Mori, Shin Yoneya, Masakazu Kohda, Yasushi Okazaki, Taro Maruyama, Akira Shimada, Kazuki Yasuda, Nao Nishida, Katsushi

A Genome-Wide Association Study for Diabetic Retinopathy in a Japanese Population: Potential Association with a Long Intergenic Non-Coding RNA

Kurihara Tomoko Morita-Ohkubo Yumi Miyashita Shigehiro Katayama Keisuke Mori Shin Yoneya Masakazu Kohda Yasushi Okazaki Taro Maruyama Akira Shimada Kazuki Yasuda Nao Nishida Katsushi Tokunaga Asako Koike

IL28B Polymorphisms and Clinical Implications for Hepatitis C Virus Infection in Uzbekistan

Aims Genome-wide association studies highlighted single nucleotide polymorphisms (SNPs) within the IFNL3/IL28B locus predict the treatment outcome for patients with HCV. Furthermore, SNPs in newly discovered IFNL4 are shown to have population-specific correlation with spontaneous clearance of HCV. The aim of this study was to examine the prevalence and clinical significance of...

Genome-wide association database developed in the Japanese Integrated Database Project

The establishment of high-throughput single-nucleotide polymorphism (SNP)-typing technologies has enabled astonishing progress to be made in genome-wide association studies (GWAS), and various novel genetic factors associated with complex diseases have been discovered. Our organization has created a public repository database (DB) to achieve a continuous and intensive management...

Identification of Novel Schizophrenia Loci by Homozygosity Mapping Using DNA Microarray Analysis

The recent development of high-resolution DNA microarrays, in which hundreds of thousands of single nucleotide polymorphisms (SNPs) are genotyped, enables the rapid identification of susceptibility genes for complex diseases. Clusters of these SNPs may show runs of homozygosity (ROHs) that can be analyzed for association with disease. An analysis of patients whose parents were...

Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria

Background It has been previously demonstrated that a single nucleotide polymorphism (SNP) in the IL13 promoter region, IL13 -1055T>C (rs1800925), was associated with susceptibility to severe malaria in Thais. In the present study, fine association mapping for a cytokine gene cluster including IL4, IL5, and IL13 on chromosome 5q31 was conducted using the same malaria subjects to...

Application of partially double-stranded DNA probes to high-throughput SNPs genotyping

We have focused on DNA strand exchange reaction (SER) with partially double-stranded (PDS) probes as a novel platform of SNPs genotyping. In this report, we elaborated the method for reliable and high-throughput SNPs typing. Competitive reactions using a couple of PDS probes designed for wild and mutant sequences significantly increase resolution efficiency to SNP types that is...

Linkage disequilibrium structure of the 5q31-33 region in a Thai population

A number of loci related to the immune response are located on human chromosomal region 5q31-33, and polymorphisms in this region have been reported to be associated with autoimmune and infectious diseases. In Southeast Asian populations, no systematic survey with dense SNP markers has been performed for the 5q31-33 region. In this study, the LD and haplotype structures for a 472...

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals

Background With improvements in genotyping technologies, genome-wide association studies with hundreds of thousands of SNPs allow the identification of candidate genetic loci for multifactorial diseases in different populations. However, genotyping errors caused by genotyping platforms or genotype calling algorithms may lead to inflation of false associations between markers and...

Association of Functional Polymorphisms in Interferon Regulatory Factor 2 (IRF2) with Susceptibility to Systemic Lupus Erythematosus: A Case-Control Association Study

Study Aya Kawasaki Hiroshi Furukawa Nao Nishida Eiji Warabi Yuya Kondo Satoshi Ito Isao Matsumoto Makio Kusaoi Hirofumi Amano Akiko Suda Shouhei Nagaoka Keigo Setoguchi Tatsuo Nagai Shunsei Hirohata Kota

C/EBPβ and RUNX2 cooperate to degrade cartilage with MMP-13 as the target and HIF-2α as the inducer in chondrocytes

To elucidate the molecular mechanism underlying the endochondral ossification process during the skeletal growth and osteoarthritis (OA) development, we examined the signal network around CCAAT/enhancer-binding protein-β (C/EBPβ, encoded by CEBPB), a potent regulator of this process. Computational predictions and a C/EBP motif-reporter assay identified RUNX2 as the most potent...