Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism

ArticleNATURE PROTOCOLS. 2(11): 2857-2864 (2007)journal articl

Lack of association of Toll-like receptor 9 gene polymorphism with Behcet's disease in Japanese patients

The definitive version is available at www.blackwell-synergy.com.ArticleTISSUE ANTIGENS. 70(1-5) 423-426 (2007)journal articl

A swollen phase observed between the liquid-crystalline phase and the interdigitated phase induced by pressure and/or adding ethanol in DPPC aqueous solution

A swollen phase, in which the mean repeat distance of lipid bilayers is larger than the other phases, is found between the liquid-crystalline phase and the interdigitated gel phase in DPPC aqueous solution. Temperature, pressure and ethanol concentration dependences of the structure were investigated by small-angle neutron scattering, and a bending rigidity of lipid bilayers was by neutron spin echo. The nature of the swollen phase is similar to the anomalous swelling reported previously. However, the temperature dependence of the mean repeat distance and the bending rigidity of lipid bilayers are different. This phase could be a precursor to the interdigitated gel phase induced by pressure and/or adding ethanol.Comment: 7 pages, 6 figure

A Systems Genetics Approach Provides a Bridge from Discovered Genetic Variants to Biological Pathways in Rheumatoid Arthritis

Genome-wide association studies (GWAS) have yielded novel genetic loci underlying common diseases. We propose a systems genetics approach to utilize these discoveries for better understanding of the genetic architecture of rheumatoid arthritis (RA). Current evidence of genetic associations with RA was sought through PubMed and the NHGRI GWAS catalog. The associations of 15 single nucleotide polymorphisms and HLA-DRB1 alleles were confirmed in 1,287 cases and 1,500 controls of Japanese subjects. Among these, HLA-DRB1 alleles and eight SNPs showed significant associations and all but one of the variants had the same direction of effect as identified in the previous studies, indicating that the genetic risk factors underlying RA are shared across populations. By receiver operating characteristic curve analysis, the area under the curve (AUC) for the genetic risk score based on the selected variants was 68.4%. For seropositive RA patients only, the AUC improved to 70.9%, indicating good but suboptimal predictive ability. A simulation study shows that more than 200 additional loci with similar effect size as recent GWAS findings or 20 rare variants with intermediate effects are needed to achieve AUC = 80.0%. We performed the random walk with restart (RWR) algorithm to prioritize genes for future mapping studies. The performance of the algorithm was confirmed by leave-one-out cross-validation. The RWR algorithm pointed to ZAP70 in the first rank, in which mutation causes RA-like autoimmune arthritis in mice. By applying the hierarchical clustering method to a subnetwork comprising RA-associated genes and top-ranked genes by the RWR, we found three functional modules relevant to RA etiology: “leukocyte activation and differentiation”, “pattern-recognition receptor signaling pathway”, and “chemokines and their receptors”

The COL1A1 gene and high myopia susceptibility in Japanese

The original publication is available at www.springerlink.com