A genome-wide association study of copy-number variation identifies putative loci associated with osteoarthritis in Koreans

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Background OA is a complex disease caused by environmental and genetic risk factors. The purpose of this study is to identify candidate copy number variations (CNVs) associated with OA. Methods We performed a genome-wide association study of CNV to identify potential loci that confer susceptibility to or protection from OA. CNV genotyping was conducted using NimbleGen HD2 3 × 720K comparative hybridization array and included samples from 371 OA patients and 467 healthy controls. The putative CNV regions identified were confirmed with a TaqMan assay. Results We identified six genomic regions associated with OA encompassing CNV loci. None of six loci had previously been reported in genome-wide association studies with OA, although a genetic analysis suggested that they have functional effects. The protein product of a candidate risk gene for obesity, TNKS, targets Wnt inhibition, and this gene was significantly associated with hand and knee OA. Copy number deletion on TNKS was associated with a 1.37-fold decreased risk for OA. In addition, CA10, which shows a strong association with osteoporosis, was also significant in our study. Copy number deletion on this gene was associated with a 1.69-fold decreased risk for OA. Conclusion We identified several CNV loci that may contribute to OA susceptibility in Koreans. Further functional investigations of these genes are warranted to fully characterize their putative association

S-1 plus oxaliplatin versus capecitabine plus oxaliplatin for the first-line treatment of patients with metastatic colorectal cancer: updated results from a phase 3 trial

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Abstract Background We report updated progression-free survival (PFS) and overall survival (OS) data from a trial that compared capecitabine plus oxaliplatin (CapeOX) versus S-1 plus oxaliplatin (SOX) for the first-line treatment of metastatic colorectal cancer. Methods This trial was a randomized, two-armed, non-inferiority phase 3 comparison of CapeOX (capecitabine 1000 mg/m2 twice daily on days 1–14 and oxaliplatin 130 mg/m2 on day 1) versus SOX (S-1 40 mg/m2 twice daily on days 1–14 and oxaliplatin 130 mg/m2 on day 1). The primary end point was to show non-inferiority of SOX relative to CapeOX in terms of PFS. Thus, a follow-up exploratory analysis of PFS and OS was performed. Results The intention to treat (ITT) population was comprised of 340 patients (SOX arm: 168 and CapeOX arm: 172). The updated median PFS was 7.1 months (95% CI 6.4-8.0) in the SOX group and 6.3 months (95% CI 4.9-6.7) in the CapeOX group (hazard ratio [HR], 0.83 [0.66-1.04], p = .10). The median OS was 19.0 months (95% CI 15.3-23.0) in the SOX group and 18.4 months (95% CI 14.1-20.7) in the CapeOX group (HR, 0.86 [0.68-1.08], p = .19). Subgroup analyses according to principal demographic factors such as sex, age, ECOG (Eastern Cooperative Oncology Group) performance status, primary tumor location, measurability, previous adjuvant therapy, number of metastatic organs, and liver metastases showed no interaction between any of these characteristics and the treatment. Conclusions Updated survival analysis shows that SOX is similar to CapeOX, confirming the initial PFS analysis. Therefore, the SOX regimen could be an alternative first-line doublet chemotherapy strategy for patients with metastatic colorectal cancer. Trial registration NCT00677443 and May 12 200

Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488–47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10−13), ALDH2/MYL2 (rs671, P = 3.40 × 10−11; rs12229654, P = 4.56 × 10−9), ITIH4 (rs2535633, P = 1.77 × 10−10) and NT5C2 (rs11191580, P = 3.83 × 10−8) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10−8) and an additional 14 at P < 1.0 × 10−3 with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity

Data from: Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches

Premise of the study: Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components. Methods: We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group. Key results: The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera Mallomonas and Synura diverging during the Early Cretaceous at 130 Ma. Mallomonas further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. Synura also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners. Conclusions: The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval

Genome-Wide Association Study Identifies Two Novel Loci with Sex-Specific Effects for Type 2 Diabetes Mellitus and Glycemic Traits in a Korean Population

BackgroundUntil recently, genome-wide association study (GWAS)-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM) or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population.MethodsWe performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842). The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500). A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively.ResultsA combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356) loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of β-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study.ConclusionOur study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population

Multigene phylogeny of <i>Synura</i> (Synurophyceae) and descriptions of four new species based on morphological and DNA evidence

<p>We used phylogenetic analyses based on multiple gene sequences (partial nr SSU and LSU rDNA, partial pt LSU rDNA, <i>psa</i>A and <i>rbc</i>L) from 148 strains (including three outgroups) and scale ultrastructure to examine phylogenetic relationships among species of the colonial genera <i>Synura</i> and <i>Tessellaria</i>. The phylogenetic tree based on the combined dataset was congruent with ultrastructural characteristics of the scales. <i>Synura</i> was divided into three major clades, two including species in section <i>Synura</i>, and one representing section <i>Peterseniae</i>. One clade, consisting of seven strains of <i>S. uvella</i> (section <i>Synura</i>), diverged at the base of the genus. The second clade consisted of the remaining species belonging to the section <i>Synura</i>. The third clade, containing organisms in the section <i>Peterseniae</i> and characterized by scales possessing a keel, was monophyletic with strong support values. Based on our findings, <i>S. uvella</i> needs to be in a separate section from other spine-bearing species, and we therefore propose new sectional ranks; <i>Synura, Peterseniae, Curtispinae</i> (presence of body scales with slender spines, tubular scales and caudal scales). We further propose four new species based on phylogenetic analyses and unique scale characters: <i>S. longitubularis</i> sp. nov., <i>S. sungminbooi</i> sp. nov., <i>S. soroconopea</i> sp. nov. and <i>S. lanceolata</i> sp. nov. Lastly, we propose a new genus name, <i>Neotessella</i>, to replace the invalid use of the name <i>Tessellaria</i>.</p

Fig2 Five gene data matrix.nex

Five gene data set (nuclear SSU, nuclear LSU, plastid LSU, plastid psaA, plastid rbcL

Fig2 Time-calibrated phylogenetic tree.tre

Figure 2. Time-calibrated phylogenetic tree for the Synurophyceae based on a five-gene dataset

Molecular Cloning, Sequence Characterization and Expression Analysis of a CD63 Homologue from the Coleopteran Beetle, Tenebrio molitor

CD63, a member of the tetraspanin membrane protein family, plays a pivotal role in cell growth, motility, signal transduction, host-pathogen interactions and cancer. In this work, the cDNA encoding CD63 homologue (TmCD63) was cloned from larvae of a coleopteran beetle, Tenebrio molitor. The cDNA is comprised of an open reading frame of 705 bp, encoding putative protein of 235 amino acid residues. In silico analysis shows that the protein has four putative transmembrane domains and one large extracellular loop. The characteristic “Cys-Cys-Gly” motif and “Cys188” residues are highly conserved in the large extracellular loop. Phylogenetic analysis of TmCD63 revealed that they belong to the insect cluster with 50%–56% identity. Analysis of spatial expression patterns demonstrated that TmCD63 mRNA is mainly expressed in gut and Malphigian tubules of larvae and the testis of the adult. Developmental expression patterns of CD63 mRNA showed that TmCD63 transcripts are detected in late larval, pupal and adult stages. Interestingly, TmCD63 transcripts are upregulated to the maximum level of 4.5 fold, in response to DAP-type peptidoglycan during the first 6 h, although other immune elicitors also caused significant increase to the transcript level at later time-points. These results suggest that CD63 might contribute to T. molitor immune response against various microbial pathogens