Predictors of the Uptake of A (H1N1) Influenza Vaccine: Findings from a Population-Based Longitudinal Study in Tokyo

BACKGROUND: Overall pandemic A (H1N1) influenza vaccination rates remain low across all nations, including Japan. To increase the rates, it is important to understand the motives and barriers for the acceptance of the vaccine. We conducted this study to determine potential predictors of the uptake of A (H1N1) influenza vaccine in a cohort of Japanese general population. METHODOLOGY/PRINCIPAL FINDINGS: By using self-administered questionnaires, this population-based longitudinal study was conducted from October 2009 to April 2010 among 428 adults aged 18-65 years randomly selected from each household residing in four wards and one city in Tokyo. Multiple logistic regression analyses were performed. Of total, 38.1% of participants received seasonal influenza vaccine during the preceding season, 57.0% had willingness to accept A (H1N1) influenza vaccine at baseline, and 12.1% had received A (H1N1) influenza vaccine by the time of follow-up. After adjustment for potential confounding variables, people who had been vaccinated were significantly more likely to be living with an underlying disease (p = 0.001), to perceive high susceptibility to influenza (p = 0.03), to have willingness to pay even if the vaccine costs ≥ US$44 (p = 0.04), to have received seasonal influenza vaccine during the preceding season (p<0.001), and to have willingness to accept A (H1N1) influenza vaccine at baseline (p<0.001) compared to those who had not been vaccinated. CONCLUSIONS/SIGNIFICANCE: While studies have reported high rates of willingness to receive A (H1N1) influenza vaccine, these rates may not transpire in the actual practices. The uptake of the vaccine may be determined by several potential factors such as perceived susceptibility to influenza and sensitivity to vaccination cost in general population

Multiple Gene Polymorphisms in the Complement Factor H Gene Are Associated with Exudative Age-Related Macular Degeneration in Chinese

PURPOSE. Variants in the complement factor H (CFH) gene have been shown to be strongly associated with age-related macular degeneration (AMD). In this study, sequence alterations in CFH were investigated in 163 Chinese patients with exudative AMD and 155 unrelated Chinese control subjects. METHODS. All the 22 CFH exons, intron-exon boundaries, and promoter sequences were screened by polymerase chain reaction and DNA sequencing. RESULTS. Fifty-eight sequence changes, 42 of them novel, were identified. Six SNPs with an allele frequency Ͼ30% were significantly associated with exudative AMD. SNP rs3753396 was novel; the rest had been reported: rs3753394, rs551397, rs800292, rs2274700, and rs1329428. Two haplotype blocks were constructed. The TG haplotype for rs551397 and rs800292 was the major haplotype that conferred a significantly increased susceptibility to exudative AMD (P corr ϭ 0.0001, OR ϭ 1.91, 95% CI ϭ 1.36 -2.68). CONCLUSIONS. The findings support prior evidence that the CFH gene is one of the AMD-associated genes. There is a different distribution pattern of CFH variants in the Chinese compared with other populations. Individual SNP and haplotype analyses revealed that the ancient alleles at the 5Ј end of CFH contribute to an increased susceptibility to exudative AMD. (Invest Ophthalmol Vis Sci. 2008;49:3312-3317) DOI:10.1167/iovs.07-1517 A ge-related macular degeneration (AMD; MIM 603075; Mendelian Inheritance in Man) is a major cause of irreversible visual impairment and blindness in people older than 65 years in developed countries. 1,2 The occurrence of AMD is pan ethnic, and a high prevalence AMD has been reported in the elderly Chinese population. 5 Therefore, a greater understanding of the primary pathophysiology is needed to advance treatment and preventive measures. The etiology of AMD is complex and multifactorial, probably resulting from interactions between environmental and multigenetic factors. 6 Genetic association studies have revealed that single nucleotide polymorphisms (SNPs) in the complement factor H gene (CFH; MIM 134370; e.g., Tyr402His) are significantly associated with susceptibility to AMD. 25 A fine-scale linkage disequilibrium mapping of AMD in the CFH region detected a point location of a causal variant between exons 1 and 2 of CFH other than exon 9 for Tyr402His. MATERIALS AND METHODS Patients and Control Subjects 21 Also recruited and given complete ophthalmic examinations were 155 unrelated control subjects, 72 men and 83 women ranging in age at recruitment from 60 to 99 years (mean Ϯ SD, 73.1 Ϯ 6.5 years). They matched the patients by age and gender and had no sign of AMD or other eye diseases, except mild myopia or senile cataract. The study protocol was approved by the Ethics Committee on Human Research, the Chinese University of Hong Kong. All the procedures used conformed to the tenets of the Declaration of Helsinki. Informed consent was obtained from all study subjects after explanation of the nature of the study. Sample Collection, PCR Amplification, DNA Sequencing, and SNP Genotyping Venous blood was obtained from each study subject, and genomic DNA was extracted with a DNA blood kit (QIAamp; Qiagen, Hilden, Germany). The promoter sequence up to Ϫ867 upstream and all coding sequences of the CFH gene, including intron-exon boundaries, were screened for sequence alterations. Primers were generated based on the GenBank sequence of CFH (NM_000186.2; http://www.ncbi. nlm.nih.gov/Genbank; provided in the public domain by the National Center for Biotechnology Information, Bethesda, MD). PCR was performed on a thermal cycler (model 9700; Applied Biosystems, Inc. [ABI], Foster City, CA) with optimized protocols 27 Statistical Analysis Hardy-Weinberg equilibrium (HWE) for each polymorphism was tested by 2 test. Allele or genotype frequencies between cases and control subjects were compared by 2 analysis or the Fisher exact test. The odds ratios (ORs) of the alleles and haplotypes were estimated by 2 test (SPSS ver.15.0; SPSS Inc., Chicago, IL). Population attributable risk (PAR) of the risk genotype was calculated with the formula f(R Ϫ 1)/R, where f is the faction of cases with the risk genotype and R is the measure of OR 8 . A pair-wise linkage disequilibrium (LD, DЈ) estimation between polymorphisms with a minor allele frequency (MAF) Ͼ 1%, and EM-based haplotype association analysis were performed with Haploview (ver. 3.32, from http://www.broad.mit.edu/mpg/ haploview/ provided in the public domain by the Broad Institute, Massachusetts Institute of Technology, Cambridge, MA). For multiple comparison, probabilities were corrected by permutation test (iterations, 10,000). Statistical significance was defined as a corrected P (P corr ) Ͻ 0.05. RESULTS CFH Variants in the Study Subjects A total of 58 sequence variations were identified, all of which followed Hardy Weinberg Equilibrium Six of the seven common variants Six SNPs were identified in the promoter, all supported decreased susceptibility to AMD Haplotype Association Analysis LD analysis revealed extension of LD throughout the CFH gene. We included SNPs with MAF Ͼ 5% and two missense changes, rs1061170 (Tyr402His) and Val837Ile, in our haplotype association analysis. Two distinct haplotype blocks were detected The haplotypes H3 and H4, which were defined by all six AMD-associated SNPs, conferred significantly reduced or increased AMD susceptibility (H3: OR ϭ 0.56, 95% CI ϭ 0.39 -0.80; H4: OR ϭ 1.63, 95% CI ϭ 1.19 -2.23). When a G allele of rs1065489 (Asp936Glu) was included in these two haplotypes, the H5, which contained all the alleles in H3, remain significantly associated with the disease (P corr ϭ 0.0012). However, when a G allele or a T allele was added to the H4, the newly constructed H6 and H7 were no longer AMD associated (P corr ϭ 0.052 and 0.177, respectively). We constructed two-allele haplotypes by using rs800292 (Val62Ile) with the uncommon SNPs rs1061170 (Tyr402His) and Val837Ile, to investigate the effects of the minor variants. H10 and H11, containing a T allele of rs1061170 (Tyr402His), remained significantly associated with AMD. However, the haplotypes containing a C allele of rs1061170 DISCUSSION Although the pathogenesis of exudative AMD has not been definitively elucidated, studies in the past few years have revealed important information on its genetic basis. Polymorphisms in the CFH gene have been shown to be AMD associated in different ethnic groups, although there are obvious differences in the occurrence of disease-susceptible SNPs between Caucasian and Oriental populations. 26 mapped a point location for a causal variant between exons 1 and 2, which approximates block 1 in our present study, suggesting that the 5Ј region of the CFH (N-terminal of factor H) is commonly associated with AMD in both Chinese and Caucasians. We found haplotype block 2 spanning a region from exon 10 to intron 15 and containing SNP rs2274700 (Ala473Ala, exon 10), which have recently been shown to have a strong association with AMD in Caucasians and Japanese. Besides the haplotypes in the two haplotype blocks, the haplotypes defined by the six common SNPs (H3, H4) were also significantly associated with exudative AMD. However, when Asp936Glu (in exon 18) was included in the at-risk haplotype H4 for association analysis, the haplotypes H6 and H7, including a G or a T allele respectively, were no longer significantly associated with the disease (P corr Ͼ 0.05). Thus, Asp936Glu is less likely to be a risk factor for exudative AMD in Chinese individuals, indicating the C-terminal of the factor H contributes less than other parts of the polypeptide to the development of exudative AMD. This observation is consistent with the findings of Hageman et al

Ciprofloxacin-resistant Salmonella enterica Typhimurium and Choleraesuis from Pigs to Humans, Taiwan

We evaluated the disk susceptibility data of 671 nontyphoid Salmonella isolates collected from different parts of Taiwan from March 2001 to August 2001 and 1,261 nontyphoid Salmonella isolates from the National Taiwan University Hospital from 1996 to 2001. Overall, ciprofloxacn resistance was found in 2.7% (18/671) of all nontyphoid Salmonella isolates, in 1.4% (5/347) of Salmonella enterica serotype Typhimurium and in 7.5% (8/107) in S. enterica serotype Choleraesuis nationwide. MICs of six newer fluoroquinolones were determined for the following isolates: 37 isolates of ciprofloxacin-resistant (human) S. enterica Typhimurium (N = 26) and Choleraesuis (N = 11), 10 isolates of ciprofloxacin-susceptible (MIC <1 μg/mL) (human) isolates of these two serotypes, and 15 swine isolates from S. enterica Choleraesuis (N = 13) and Typhmurium (N = 2) with reduced susceptibility to ciprofloxacin (MIC >0.12 μg/mL). Sequence analysis of the gryA, gyrB, parC, parE, and acrR genes, ciprofloxacin accumulation; and genotypes generated by pulsed-field gel electrophoresis with three restriction enzymes (SpeI, XbaI, and BlnI) were performed. All 26 S. enterica Typhimurium isolates from humans and pigs belonged to genotype I. For S. enterica Choleraesuis isolates, 91% (10/11) of human isolates and 54% (7/13) of swine isolates belonged to genotype B. These two genotypes isolates from humans all exhibited a high-level of resistance to ciprofloxacin (MIC 16–64 μg/mL). They had two-base substitutions in the gyrA gene at codons 83 (Ser83Phe) and 87 (Asp87Gly or Asp87Asn) and in the parC gene at codon 80 (Ser80Arg, Ser80Ile, or Ser84Lys). Our investigation documented that not only did these two S. enterica isolates have a high prevalence of ciprofloxacin resistance nationwide but also that some closely related ciprofloxacin-resistant strains are disseminated from pigs to humans

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

10.1186/1471-2164-12-174BMC Genomics12-BGME

Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma

Background: With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology. Methodology: The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients. Principal Findings: A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206) play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122) without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e. g., cell cycle and apoptosis pathways) and cell communication (e. g., focal adhesion and ECM-receptor interaction) were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of similar to 50 ccRCC patients. Conclusions: Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC