Search

The ability to computationally predict the effects of toxic compounds on humans could help address the deficiencies of current chemical safety testing. Here, we report the results from a community-based DREAM challenge to predict toxicities of environmental compounds with potential adverse health effects for human populations. We measured the cytotoxicity of 156 compounds in 884 lymphoblastoid cell lines for which genotype and transcriptional data are available as part of the Tox21 1000 Genomes Project. The challenge participants developed algorithms to predict interindividual variability of toxic response from genomic profiles and population-level cytotoxicity data from structural attributes of the compounds. 179 submitted predictions were evaluated against an experimental data set to which participants were blinded. Individual cytotoxicity predictions were better than random, with modest correlations (Pearson's r < 0.28), consistent with complex trait genomic prediction. In contrast, predictions of population-level response to different compounds were higher (r < 0.66). The results highlight the possibility of predicting health risks associated with unknown compounds, although risk estimation accuracy remains suboptimal.

Background: Metabolomic evaluation of cystic fibrosis (CF) airway secretions could identify metabolites and metabolic pathways involved in neutrophilic airway inflammation that could serve as biomarkers and therapeutic targets., Methods: Mass spectrometry (MS)-based metabolomics was performed on a discovery set of BAL fluid samples from 25 children with CF, and targeted MS methods were used to identify and quantify metabolites related to neutrophilic inflammation. A biomarker panel of these metabolites was then compared with neutrophil counts and clinical markers in independent validation sets of lavage from children with CF and adults with COPD compared with control subjects., Results: Of the 7,791 individual peaks detected by positive-mode MS metabolomics discovery profiling, 338 were associated with neutrophilic inflammation. Targeted MS determined that many of these peaks were generated by metabolites from pathways related to the metabolism of purines, polyamines, proteins, and nicotinamide. Analysis of the independent validation sets verified that, in subjects with CF or COPD, several metabolites, particularly those from purine metabolism and protein catabolism pathways, were strongly correlated with neutrophil counts and were related to clinical markers, including airway infection and lung function., Conclusions: MS metabolomics identified multiple metabolic pathways associated with neutrophilic airway inflammation. These findings provide insight into disease pathophysiology and can serve as the basis for developing disease biomarkers and therapeutic interventions for airways diseases.

A number of biomedical problems require performing many hypothesis tests, with an attendant need to apply stringent thresholds. Often the data take the form of a series of predictor vectors, each of which must be compared with a single response vector, perhaps with nuisance covariates. Parametric tests of association are often used, but can result in inaccurate type I error at the extreme thresholds, even for large sample sizes. Furthermore, standard two-sided testing can reduce power compared with the doubled [Formula: see text]-value, due to asymmetry in the null distribution. Exact (permutation) testing is attractive, but can be computationally intensive and cumbersome. We present an approximation to exact association tests of trend that is accurate and fast enough for standard use in high-throughput settings, and can easily provide standard two-sided or doubled [Formula: see text]-values. The approach is shown to be equivalent under permutation to likelihood ratio tests for the most commonly used generalized linear models (GLMs). For linear regression, covariates are handled by working with covariate-residualized responses and predictors. For GLMs, stratified covariates can be handled in a manner similar to exact conditional testing. Simulations and examples illustrate the wide applicability of the approach. The accompanying mcc package is available on CRAN http://cran.r-project.org/web/packages/mcc/index.html., (© The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

There is strong epidemiologic evidence linking chronic exposure to inorganic arsenic (iAs) to myriad adverse health effects, including cancer of the bladder. We set out to identify DNA methylation patterns associated with arsenic and its metabolites in exfoliated urothelial cells (EUCs) that originate primarily from the urinary bladder, one of the targets of arsenic-induced carcinogenesis. Genome-wide, gene-specific promoter DNA methylation levels were assessed in EUCs from 46 residents of Chihuahua, Mexico, and the relationship was examined between promoter methylation profiles and the intracellular concentrations of total arsenic and arsenic species. A set of 49 differentially methylated genes was identified with increased promoter methylation associated with EUC tAs, iAs, and/or monomethylated As (MMAs) enriched for their roles in metabolic disease and cancer. Notably, no genes had differential methylation associated with EUC dimethylated As (DMAs), suggesting that DMAs may influence DNA methylation-mediated urothelial cell responses to a lesser extent than iAs or MMAs. Further analysis showed that 22 of the 49 arsenic-associated genes (45%) are also differentially methylated in bladder cancer tissue identified using The Cancer Genome Atlas repository. Both the arsenic- and cancer-associated genes are enriched for the binding sites of common transcription factors known to play roles in carcinogenesis, demonstrating a novel potential mechanistic link between iAs exposure and bladder cancer.

RNF170 is an endoplasmic reticulum membrane ubiquitin ligase that contributes to the ubiquitination of activated inositol 1,4,5-trisphosphate (IP3) receptors, and also, when point mutated (arginine to cysteine at position 199), causes autosomal dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. Here we demonstrate that this point mutation inhibits RNF170 expression and signaling via IP3 receptors. Inhibited expression of mutant RNF170 was seen in cells expressing exogenous RNF170 constructs and in ADSA lymphoblasts, and appears to result from enhanced RNF170 autoubiquitination and proteasomal degradation. The basis for these effects was probed via additional point mutations, revealing that ionic interactions between charged residues in the transmembrane domains of RNF170 are required for protein stability. In ADSA lymphoblasts, platelet-activating factor-induced Ca(2+) mobilization was significantly impaired, whereas neither Ca(2+) store content, IP3 receptor levels, nor IP3 production were altered, indicative of a functional defect at the IP3 receptor locus, which may be the cause of neurodegeneration. CRISPR/Cas9-mediated genetic deletion of RNF170 showed that RNF170 mediates the addition of all of the ubiquitin conjugates known to become attached to activated IP3 receptors (monoubiquitin and Lys(48)- and Lys(63)-linked ubiquitin chains), and that wild-type and mutant RNF170 have apparently identical ubiquitin ligase activities toward IP3 receptors. Thus, the Ca(2+) mobilization defect seen in ADSA lymphoblasts is apparently not due to aberrant IP3 receptor ubiquitination. Rather, the defect likely reflects abnormal ubiquitination of other substrates, or adaptation to the chronic reduction in RNF170 levels., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)

To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.

Transcriptional regulation and posttranscriptional processing underlie many cellular and organismal phenotypes. We used RNA sequence data generated by Genotype-Tissue Expression (GTEx) project to investigate the patterns of transcriptome variation across individuals and tissues. Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples. These signatures are dominated by a relatively small number of genes—which is most clearly seen in blood—though few are exclusive to a particular tissue and vary more across tissues than individuals. Genes exhibiting high interindividual expression variation include disease candidates associated with sex, ethnicity, and age. Primary transcription is the major driver of cellular specificity, with splicing playing mostly a complementary role; except for the brain, which exhibits a more divergent splicing program. Variation in splicing, despite its stochasticity, may play in contrast a comparatively greater role in defining individual phenotypes., (Copyright © 2015, American Association for the Advancement of Science.)

Background: Understanding of human variation in toxicity to environmental chemicals remains limited, so human health risk assessments still largely rely on a generic 10-fold factor (10½ each for toxicokinetics and toxicodynamics) to account for sensitive individuals or subpopulations., Objectives: We tested a hypothesis that population-wide in vitro cytotoxicity screening can rapidly inform both the magnitude of and molecular causes for interindividual toxicodynamic variability., Methods: We used 1,086 lymphoblastoid cell lines from the 1000 Genomes Project, representing nine populations from five continents, to assess variation in cytotoxic response to 179 chemicals. Analysis included assessments of population variation and heritability, and genome-wide association mapping, with attention to phenotypic relevance to human exposures., Results: For about half the tested compounds, cytotoxic response in the 1% most "sensitive" individual occurred at concentrations within a factor of 10½ (i.e., approximately 3) of that in the median individual; however, for some compounds, this factor was > 10. Genetic mapping suggested important roles for variation in membrane and transmembrane genes, with a number of chemicals showing association with SNP rs13120371 in the solute carrier SLC7A11, previously implicated in chemoresistance., Conclusions: This experimental approach fills critical gaps unaddressed by recent large-scale toxicity testing programs, providing quantitative, experimentally based estimates of human toxicodynamic variability, and also testable hypotheses about mechanisms contributing to interindividual variation.

A polycyclic aromatic hydrocarbon-degrading bacterium designated strain Ca6, a member of the family Rhodocyclaceae and a representative of the uncharacterized pyrene group 1 (PG1), was isolated and its genome sequenced. The presence of several genes suspected to be associated with PG1 was confirmed, and additional genes for aromatic compound metabolism were detected., (Copyright © 2015 Singleton et al.)

Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease., (Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Hematopoietic stem cell transplantation is a high-risk procedure that is offered, with curative intent, to patients with malignant and nonmalignant disease. The clinical benefits of personalization of therapy by genotyping have been demonstrated by the reduction in transplant related mortality from donor-recipient HLA matching. However, defining the relationship between genotype and transplant conditioning agents is yet to be translated into clinical practice. A number of the therapeutic agents used in stem cell transplant preparative regimens have pharmacokinetic parameters that predict benefit of incorporating pharmacogenomic data into dosing strategies. Busulfan, cyclophosphamide, thio-TEPA and etoposide have well-described drug metabolism pathways, however candidate gene studies have identified there is a gap in the identification of pharmacogenomic data that can be used to improve transplant outcomes. Incorporating pharmacogenomics into pharmacokinetic modeling may demonstrate the therapeutic benefits of genotyping in transplant preparative regimen agents.

The development of high-throughput biomedical technologies has led to increased interest in the analysis of high-dimensional data where the number of features is much larger than the sample size. In this paper, we investigate principal component analysis under the ultra-high dimensional regime, where both the number of features and the sample size increase as the ratio of the two quantities also increases. We bridge the existing results from the finite and the high-dimension low sample size regimes, embedding the two regimes in a more general framework. We also numerically demonstrate the universal application of the results from the finite regime.

Background: Quantitative estimation of toxicokinetic variability in the human population is a persistent challenge in risk assessment of environmental chemicals. Traditionally, interindividual differences in the population are accounted for by default assumptions or, in rare cases, are based on human toxicokinetic data., Objectives: We evaluated the utility of genetically diverse mouse strains for estimating toxicokinetic population variability for risk assessment, using trichloroethylene (TCE) metabolism as a case study., Methods: We used data on oxidative and glutathione conjugation metabolism of TCE in 16 inbred and 1 hybrid mouse strains to calibrate and extend existing physiologically based pharmacokinetic (PBPK) models. We added one-compartment models for glutathione metabolites and a two-compartment model for dichloroacetic acid (DCA). We used a Bayesian population analysis of interstrain variability to quantify variability in TCE metabolism., Results: Concentration-time profiles for TCE metabolism to oxidative and glutathione conjugation metabolites varied across strains. Median predictions for the metabolic flux through oxidation were less variable (5-fold range) than that through glutathione conjugation (10-fold range). For oxidative metabolites, median predictions of trichloroacetic acid production were less variable (2-fold range) than DCA production (5-fold range), although the uncertainty bounds for DCA exceeded the predicted variability., Conclusions: Population PBPK modeling of genetically diverse mouse strains can provide useful quantitative estimates of toxicokinetic population variability. When extrapolated to lower doses more relevant to environmental exposures, mouse population-derived variability estimates for TCE metabolism closely matched population variability estimates previously derived from human toxicokinetic studies with TCE, highlighting the utility of mouse interstrain metabolism studies for addressing toxicokinetic variability.

Background: Benchmark dose (BMD) modeling computes the dose associated with a prespecified response level. While offering advantages over traditional points of departure (PODs), such as no-observed-adverse-effect-levels (NOAELs), BMD methods have lacked consistency and transparency in application, interpretation, and reporting in human health assessments of chemicals., Objectives: We aimed to apply a standardized process for conducting BMD modeling to reduce inconsistencies in model fitting and selection., Methods: We evaluated 880 dose-response data sets for 352 environmental chemicals with existing human health assessments. We calculated benchmark doses and their lower limits [10% extra risk, or change in the mean equal to 1 SD (BMD/L10/1SD)] for each chemical in a standardized way with prespecified criteria for model fit acceptance. We identified study design features associated with acceptable model fits., Results: We derived values for 255 (72%) of the chemicals. Batch-calculated BMD/L10/1SD values were significantly and highly correlated (R2 of 0.95 and 0.83, respectively, n = 42) with PODs previously used in human health assessments, with values similar to reported NOAELs. Specifically, the median ratio of BMDs10/1SD:NOAELs was 1.96, and the median ratio of BMDLs10/1SD:NOAELs was 0.89. We also observed a significant trend of increasing model viability with increasing number of dose groups., Conclusions: BMD/L10/1SD values can be calculated in a standardized way for use in health assessments on a large number of chemicals and critical effects. This facilitates the exploration of health effects across multiple studies of a given chemical or, when chemicals need to be compared, providing greater transparency and efficiency than current approaches.

We assessed gene expression profiles in 2,752 twins, using a classic twin design to quantify expression heritability and quantitative trait loci (eQTLs) in peripheral blood. The most highly heritable genes (∼777) were grouped into distinct expression clusters, enriched in gene-poor regions, associated with specific gene function or ontology classes, and strongly associated with disease designation. The design enabled a comparison of twin-based heritability to estimates based on dizygotic identity-by-descent sharing and distant genetic relatedness. Consideration of sampling variation suggests that previous heritability estimates have been upwardly biased. Genotyping of 2,494 twins enabled powerful identification of eQTLs, which we further examined in a replication set of 1,895 unrelated subjects. A large number of non-redundant local eQTLs (6,756) met replication criteria, whereas a relatively small number of distant eQTLs (165) met quality control and replication standards. Our results provide a new resource toward understanding the genetic control of transcription.

Cadmium (Cd) is prevalent in the environment yet understudied as a developmental toxicant. Cd partially crosses the placental barrier from mother to fetus and is linked to detrimental effects in newborns. Here we examine the relationship between levels of Cd during pregnancy and 5-methylcytosine (5mC) levels in leukocyte DNA collected from 17 mother-newborn pairs. The methylation of cytosines is an epigenetic mechanism known to impact transcriptional signaling and influence health endpoints. A methylated cytosine-guanine (CpG) island recovery assay was used to assess over 4.6 million sites spanning 16,421 CpG islands. Exposure to Cd was classified for each mother-newborn pair according to maternal blood levels and compared with levels of cotinine. Subsets of genes were identified that showed altered DNA methylation levels in their promoter regions in fetal DNA associated with levels of Cd (n = 61), cotinine (n = 366), or both (n = 30). Likewise, in maternal DNA, differentially methylated genes were identified that were associated with Cd (n = 92) or cotinine (n = 134) levels. While the gene sets were largely distinct between maternal and fetal DNA, functional similarities at the biological pathway level were identified including an enrichment of genes that encode for proteins that control transcriptional regulation and apoptosis. Furthermore, conserved DNA motifs with sequence similarity to specific transcription factor binding sites were identified within the CpG islands of the gene sets. This study provides evidence for distinct patterns of DNA methylation or "footprints" in fetal and maternal DNA associated with exposure to Cd.

Background: Genomes of men and women differ in only a limited number of genes located on the sex chromosomes, whereas the transcriptome is far more sex-specific. Identification of sex-biased gene expression will contribute to understanding the molecular basis of sex-differences in complex traits and common diseases., Results: Sex differences in the human peripheral blood transcriptome were characterized using microarrays in 5,241 subjects, accounting for menopause status and hormonal contraceptive use. Sex-specific expression was observed for 582 autosomal genes, of which 57.7% was upregulated in women (female-biased genes). Female-biased genes were enriched for several immune system GO categories, genes linked to rheumatoid arthritis (16%) and genes regulated by estrogen (18%). Male-biased genes were enriched for genes linked to renal cancer (9%). Sex-differences in gene expression were smaller in postmenopausal women, larger in women using hormonal contraceptives and not caused by sex-specific eQTLs, confirming the role of estrogen in regulating sex-biased genes., Conclusions: This study indicates that sex-bias in gene expression is extensive and may underlie sex-differences in the prevalence of common diseases.

Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes show promise for screening during early drug development. Here, we tested a hypothesis that in vitro assessment of multiple cardiomyocyte physiological parameters enables predictive and mechanistically-interpretable evaluation of cardiotoxicity in a high-throughput format. Human iPSC-derived cardiomyocytes were exposed for 30 min or 24 h to 131 drugs, positive (107) and negative (24) for in vivo cardiotoxicity, in up to 6 concentrations (3 nM to 30 uM) in 384-well plates. Fast kinetic imaging was used to monitor changes in cardiomyocyte function using intracellular Ca(2+) flux readouts synchronous with beating, and cell viability. A number of physiological parameters of cardiomyocyte beating, such as beat rate, peak shape (amplitude, width, raise, decay, etc.) and regularity were collected using automated data analysis. Concentration-response profiles were evaluated using logistic modeling to derive a benchmark concentration (BMC) point-of-departure value, based on one standard deviation departure from the estimated baseline in vehicle (0.3% dimethyl sulfoxide)-treated cells. BMC values were used for cardiotoxicity classification and ranking of compounds. Beat rate and several peak shape parameters were found to be good predictors, while cell viability had poor classification accuracy. In addition, we applied the Toxicological Prioritization Index (ToxPi) approach to integrate and display data across many collected parameters, to derive "cardiosafety" ranking of tested compounds. Multi-parameter screening of beating profiles allows for cardiotoxicity risk assessment and identification of specific patterns defining mechanism-specific effects. These data and analysis methods may be used widely for compound screening and early safety evaluation in drug development., (© 2013.)

Objective: This study aims to analyse the relationship between seven health practices, oral health behaviors, and oral health status in community dwelling elderly Thai., Materials and Methods: The subjects were 612 elderly people (mean age = 68.8 ± 5.9 years). Questionnaires survey about sociodemographics, self-reported seven health practices and oral health behaviors were conducted by trained interviewers. Oral examinations investigated the number of teeth present, decayed teeth, periodontal status and functional tooth units (FTUs). Oral malodor was assessed by Organoleptic Test, and unstimulated saliva was collected for 5 min., Results: Five health practices (smoking, drinking, physical activity, breakfast and weight maintenance) were significantly related with oral health behaviors. ancova analysis demonstrated the following significant associations: (i) smoking behavior with number of teeth present, number of FTUs, decayed teeth, periodontal disease, oral malodor and salivary flow rate, (ii) drinking alcohol behavior with number of teeth present, number of FTUs, periodontal disease, oral malodor and salivary flow rate, (iii) eating breakfast behavior with periodontal disease, oral malodor and salivary flow rate, (iv) eating between-meal snack with number of teeth present, number of FTUs, decayed teeth and periodontal disease, (v) maintaining weight with number of teeth present, number of FTUs, periodontal disease and oral malodor, (vi) sleeping with number of teeth present, number of FTUs, periodontal disease, oral malodor and salivary flow rate, (vii) physical activity with periodontal disease and salivary flow rate., Conclusion: Good health practices were related with good oral health behaviors. Moreover, general health practices were associated with the clinical oral health status such as number of teeth present, decayed teeth, FTUs, periodontal disease, oral malodor and salivary flow rate. The elderly with good general health practices were considered to have good oral health status. Improving general health habits are suggested to lead to better oral health for the elderly, and vice versa., (© 2012 John Wiley & Sons A/S and The Gerodontology Society. Published by John Wiley & Sons Ltd.)

In the past few years, a plethora of methods for rare variant association with phenotype have been proposed. These methods aggregate information from multiple rare variants across genomic region(s), but there is little consensus as to which method is most effective. The weighting scheme adopted when aggregating information across variants is one of the primary determinants of effectiveness. Here we present a systematic evaluation of multiple weighting schemes through a series of simulations intended to mimic large sequencing studies of a quantitative trait. We evaluate existing phenotype-independent and phenotype-dependent methods, as well as weights estimated by penalized regression approaches including Lasso, Elastic Net, and SCAD. We find that the difference in power between phenotype-dependent schemes is negligible when high-quality functional annotations are available. When functional annotations are unavailable or incomplete, all methods suffer from power loss; however, the variable selection methods outperform the others at the cost of increased computational time. Therefore, in the absence of good annotation, we recommend variable selection methods (which can be viewed as "statistical annotation") on top of regions implicated by a phenotype-independent weighting scheme. Further, once a region is implicated, variable selection can help to identify potential causal single nucleotide polymorphisms for biological validation. These findings are supported by an analysis of a high coverage targeted sequencing study of 1,898 individuals., (© 2013 WILEY PERIODICALS, INC.)

Diabetes is a common age-dependent complication of cystic fibrosis (CF) that is strongly influenced by modifier genes. We conducted a genome-wide association study in 3,059 individuals with CF (644 with CF-related diabetes [CFRD]) and identified single nucleotide polymorphisms (SNPs) within and 5' to the SLC26A9 gene that associated with CFRD (hazard ratio [HR] 1.38; P = 3.6 × 10(-8)). Replication was demonstrated in 694 individuals (124 with CFRD) (HR, 1.47; P = 0.007), with combined analysis significant at P = 9.8 × 10(-10). SLC26A9 is an epithelial chloride/bicarbonate channel that can interact with the CF transmembrane regulator (CFTR), the protein mutated in CF. We also hypothesized that common SNPs associated with type 2 diabetes also might affect risk for CFRD. A previous association of CFRD with SNPs in TCF7L2 was replicated in this study (P = 0.004; combined analysis P = 3.8 × 10(-6)), and type 2 diabetes SNPs at or near CDKAL1, CDKN2A/B, and IGF2BP2 were associated with CFRD (P < 0.004). These five loci accounted for 8.3% of the phenotypic variance in CFRD onset and had a combined population-attributable risk of 68%. Diabetes is a highly prevalent complication of CF, for which susceptibility is determined in part by variants at SLC26A9 (which mediates processes proximate to the CF disease-causing gene) and at four susceptibility loci for type 2 diabetes in the general population.

Bok is a member of the Bcl-2 protein family that controls intrinsic apoptosis. Bok is most closely related to the pro-apoptotic proteins Bak and Bax, but in contrast to Bak and Bax, very little is known about its cellular role. Here we report that Bok binds strongly and constitutively to inositol 1,4,5-trisphosphate receptors (IP3Rs), proteins that form tetrameric calcium channels in the endoplasmic reticulum (ER) membrane and govern the release of ER calcium stores. Bok binds most strongly to IP3R1 and IP3R2, and barely to IP3R3, and essentially all cellular Bok is IP3R bound in cells that express substantial amounts of IP3Rs. Binding to IP3Rs appears to be mediated by the putative BH4 domain of Bok and the docking site localizes to a small region within the coupling domain of IP3Rs (amino acids 1895-1903 of IP3R1) that is adjacent to numerous regulatory sites, including sites for proteolysis. With regard to the possible role of Bok-IP3R binding, the following was observed: (i) Bok does not appear to control the ability of IP3Rs to release ER calcium stores, (ii) Bok regulates IP3R expression, (iii) persistent activation of inositol 1,4,5-trisphosphate-dependent cell signaling causes Bok degradation by the ubiquitin-proteasome pathway, in a manner that parallels IP3R degradation, and (iv) Bok protects IP3Rs from proteolysis, either by chymotrypsin in vitro or by caspase-3 in vivo during apoptosis. Overall, these data show that Bok binds strongly and constitutively to IP3Rs and that the most significant consequence of this binding appears to be protection of IP3Rs from proteolysis. Thus, Bok may govern IP3R cleavage and activity during apoptosis.

Resampling-based expression pathway analysis techniques have been shown to preserve type I error rates, in contrast to simple gene-list approaches that implicitly assume the independence of genes in ranked lists. However, resampling is intensive in computation time and memory requirements. We describe accurate analytic approximations to permutations of score statistics, including novel approaches for Pearson's correlation, and summed score statistics, that have good performance for even relatively small sample sizes. Our approach preserves the essence of permutation pathway analysis, but with greatly reduced computation. Extensions for inclusion of covariates and censored data are described, and we test the performance of our procedures using simulations based on real datasets. These approaches have been implemented in the new R package safeExpress.

The dose-response relationship for biomarkers of exposure (N(2)-ethylidene-dG adducts) and effect (cell survival and micronucleus formation) was determined across 4.5 orders of magnitude (50nM-2mM) using [(13)C2]-acetaldehyde exposures to human lymphoblastoid TK6 cells for 12h. There was a clear increase in exogenous N (2)-ethylidene-dG formation at exposure concentrations ≥ 1µM, whereas the endogenous adducts remained nearly constant across all exposure concentrations, with an average of 3.0 adducts/10(7) dG. Exogenous adducts were lower than endogenous adducts at concentrations ≤ 10µM and were greater than endogenous adducts at concentrations ≥ 250µM. When the endogenous and exogenous adducts were summed together, statistically significant increases in total adduct formation over the endogenous background occurred at 50µM. Cell survival and micronucleus formation were monitored across the exposure range and statistically significant decreases in cell survival and increases in micronucleus formation occurred at ≥ 1000µM. This research supports the hypothesis that endogenously produced reactive species, including acetaldehyde, are always present and constitute the majority of the observed biological effects following very low exposures to exogenous acetaldehyde. These data can replace default assumptions of linear extrapolation to very low doses of exogenous acetaldehyde for risk prediction.

Motivation: Scientists and regulators are often faced with complex decisions, where use of scarce resources must be prioritized using collections of diverse information. The Toxicological Prioritization Index (ToxPi™) was developed to enable integration of multiple sources of evidence on exposure and/or safety, transformed into transparent visual rankings to facilitate decision making. The rankings and associated graphical profiles can be used to prioritize resources in various decision contexts, such as testing chemical toxicity or assessing similarity of predicted compound bioactivity profiles. The amount and types of information available to decision makers are increasing exponentially, while the complex decisions must rely on specialized domain knowledge across multiple criteria of varying importance. Thus, the ToxPi bridges a gap, combining rigorous aggregation of evidence with ease of communication to stakeholders., Results: An interactive ToxPi graphical user interface (GUI) application has been implemented to allow straightforward decision support across a variety of decision-making contexts in environmental health. The GUI allows users to easily import and recombine data, then analyze, visualize, highlight, export and communicate ToxPi results. It also provides a statistical metric of stability for both individual ToxPi scores and relative prioritized ranks., Availability: The ToxPi GUI application, complete user manual and example data files are freely available from http://comptox.unc.edu/toxpi.php.

It has been repeatedly shown that in case-control association studies, analysis of a secondary trait which ignores the original sampling scheme can produce highly biased risk estimates. Although a number of approaches have been proposed to properly analyze secondary traits, most approaches fail to reproduce the marginal logistic model assumed for the original case-control trait and/or do not allow for interaction between secondary trait and genotype marker on primary disease risk. In addition, the flexible handling of covariates remains challenging. We present a general retrospective likelihood framework to perform association testing for both binary and continuous secondary traits which respects marginal models and incorporates the interaction term. We provide a computational algorithm, based on a reparameterized approximate profile likelihood, for obtaining the maximum likelihood (ML) estimate and its standard error for the genetic effect on secondary trait, in presence of covariates. For completeness we also present an alternative pseudo-likelihood method for handling covariates. We describe extensive simulations to evaluate the performance of the ML estimator in comparison with the pseudo-likelihood and other competing methods.

Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented.

The Mantel and Knox space-time clustering statistics are popular tools to establish transmissibility of a disease and detect outbreaks. The most commonly used null distributional approximations may provide poor fits, and researchers often resort to direct sampling from the permutation distribution. However, the exact first four moments for these statistics are available, and Pearson distributional approximations are often effective. Thus, our first goal is to clarify the literature and to make these tools more widely available. In addition, by rewriting terms in the statistics we obtain the exact first four permutation moments for the most commonly used quadratic form statistics, which need not be positive definite. The extension of this work to quadratic forms greatly expands the utility of density approximations for these problems, including for high-dimensional applications, where the statistics must be extreme in order to exceed stringent testing thresholds. We demonstrate the methods using examples from the investigation of disease transmission in cattle, the association of a gene expression pathway with breast cancer survival, regional genetic association with cystic fibrosis lung disease, and hypothesis testing for smoothed local linear regression.

Australia has a complex history of providing public dental services to its communities. From the early days of Colonial settlement, the provision of dental care to the Australian public has largely been driven and influenced by organized groups and associations of dentists. The Constitution of Australia, under Section 51 xxiii A, allows for the Commonwealth to provide for medical and dental services. Unlike the United Kingdom, however, dental services have not been embedded into a universal national health service agenda. In 1974, that the Australian Government through the Australian School Dental Program provided the first funding and national direction for public dental services - and that, limited to children. The Commonwealth Dental Health Program 1993-1997 was the second national endeavor to provide public dental services, this time to financially disadvantaged adults. Since that time, public dental service responsibility has been shuttled between States/Territories and the Commonwealth. A new paradigm for public dental services in Australia requires strong Commonwealth leadership, as well as the commitment of State and Territories and the organized dental profession. The National Health and Hospitals Reform Commission provided the most recent scenario for a radical change in mission. This paper canvases the competing roles of strategic, functional, and structural issues in relationship to social network and policy issues, which must be recognized if Australians truly seek to reform public dental services., (© 2012 John Wiley & Sons A/S.)

Exome sequencing has become a powerful and effective strategy for the discovery of genes underlying Mendelian disorders. However, use of exome sequencing to identify variants associated with complex traits has been more challenging, partly because the sample sizes needed for adequate power may be very large. One strategy to increase efficiency is to sequence individuals who are at both ends of a phenotype distribution (those with extreme phenotypes). Because the frequency of alleles that contribute to the trait are enriched in one or both phenotype extremes, a modest sample size can potentially be used to identify novel candidate genes and/or alleles. As part of the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP), we used an extreme phenotype study design to discover that variants in DCTN4, encoding a dynactin protein, are associated with time to first P. aeruginosa airway infection, chronic P. aeruginosa infection and mucoid P. aeruginosa in individuals with cystic fibrosis.

Objective: To investigate oral hygiene and periodontal disease in residents of Victoria nursing homes., Background:   The Australian population is ageing with a growing proportion of elderly Australians living in nursing homes. With declining edentulism rates, periodontal disease is becoming more prevalent in this population., Materials and Methods: A total of 275 dentate residents from 31 Victorian nursing homes had a questionnaire and clinical examination using the Visual Plaque Index and a modified Community Periodontal Index., Results: Self-reported oral hygiene habits of residents were poor, with less than one-third of residents cleaning their teeth twice daily or more. Periodontal health was found to be extremely poor, and the prevalence of 4 mm+ periodontal pockets was 35.6%, with 10.2% having 6 mm+ pockets. Logistic regression found that age, gender, number of teeth present and oral hygiene were all strongly associated with the prevalence of 4 mm+ periodontal pockets., Conclusion: Poor oral hygiene and the presence of significant plaque and calculus were common findings in this study. Periodontal diseases are a significant problem for residents in nursing homes. Addressing this health issue will require improved training for carers and better access to appropriate dental services., (© 2010 The Gerodontology Society and John Wiley & Sons A/S.)

Objectives: The aim of this project was to investigate edentulism and dental caries in nursing home residents in Victoria, Australia., Background: The Australian population is ageing with a growing number of people living in nursing homes. These residents are at increased risk for dental caries, have more teeth present now than at any time in the past 50 years and often have difficulty maintaining adequate oral hygiene., Materials and Methods: Clinical dental examinations were conducted at 31 nursing homes in Melbourne and regional Victoria between May 2005 and June 2006. A total of 510 residents were examined out of 1345 eligible participants. Socio-demographic and medical history was collected via questionnaire., Results: Just over half of the residents were dentate (53.9%), and dentate residents had a mean of 14.4 teeth present and 2.66 untreated decayed teeth. Residents who required total assistance with oral hygiene had more decayed teeth and fewer filled teeth than residents who did not require assistance., Conclusions: Nursing home residents in Victoria are retaining an increasing number of natural teeth and have more tooth surfaces at risk for dental caries. Untreated dental caries was a significant problem for residents, particularly for those who are dependent on others for their daily oral hygiene care., (© 2011 The Gerodontology Society and John Wiley & Sons A/S.)

Variants associated with meconium ileus in cystic fibrosis were identified in 3,763 affected individuals by genome-wide association study (GWAS). Five SNPs at two loci near SLC6A14 at Xq23-24 (minimum P = 1.28 × 10(-12) at rs3788766) and SLC26A9 at 1q32.1 (minimum P = 9.88 × 10(-9) at rs4077468) accounted for ~5% of phenotypic variability and were replicated in an independent sample of affected individuals (n = 2,372; P = 0.001 and 0.0001, respectively). By incorporating the knowledge that disease-causing mutations in CFTR alter electrolyte and fluid flux across surface epithelium into a hypothesis-driven GWAS (GWAS-HD), we identified associations with the same SNPs in SLC6A14 and SLC26A9 and established evidence for the involvement of SNPs in a third solute carrier gene, SLC9A3. In addition, GWAS-HD provided evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides (P = 0.0002; testing of 155 apical membrane genes jointly and in replication, P = 0.022). These findings suggest that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis.

A shift in toxicity testing from in vivo to in vitro may efficiently prioritize compounds, reveal new mechanisms, and enable predictive modeling. Quantitative high-throughput screening (qHTS) is a major source of data for computational toxicology, and our goal in this study was to aid in the development of predictive in vitro models of chemical-induced toxicity, anchored on interindividual genetic variability. Eighty-one human lymphoblast cell lines from 27 Centre d'Etude du Polymorphisme Humain trios were exposed to 240 chemical substances (12 concentrations, 0.26nM-46.0μM) and evaluated for cytotoxicity and apoptosis. qHTS screening in the genetically defined population produced robust and reproducible results, which allowed for cross-compound, cross-assay, and cross-individual comparisons. Some compounds were cytotoxic to all cell types at similar concentrations, whereas others exhibited interindividual differences in cytotoxicity. Specifically, the qHTS in a population-based human in vitro model system has several unique aspects that are of utility for toxicity testing, chemical prioritization, and high-throughput risk assessment. First, standardized and high-quality concentration-response profiling, with reproducibility confirmed by comparison with previous experiments, enables prioritization of chemicals for variability in interindividual range in cytotoxicity. Second, genome-wide association analysis of cytotoxicity phenotypes allows exploration of the potential genetic determinants of interindividual variability in toxicity. Furthermore, highly significant associations identified through the analysis of population-level correlations between basal gene expression variability and chemical-induced toxicity suggest plausible mode of action hypotheses for follow-up analyses. We conclude that as the improved resolution of genetic profiling can now be matched with high-quality in vitro screening data, the evaluation of the toxicity pathways and the effects of genetic diversity are now feasible through the use of human lymphoblast cell lines.

Objectives: This study was to analyze the association of hyposalivation with oral function, nutritional status and oral health in community-dwelling elderly Thai., Method: The subjects were 612 elderly people (mean age = 68.8, SD 5.9 years). Oral function (tasting, speaking, swallowing and chewing) and Mini Nutritional Assessment (MNA) were evaluated. Oral examination investigated teeth and periodontal status. Both unstimulated and stimulated whole saliva were collected for 5 minutes., Results: Among all subjects, 14.4 % were classified within the hyposalivation. Hyposalivation was associated with gender, systemic disease, medication, and smoking. Subjects within the hyposalivation group had a higher number of decayed teeth and a higher prevalence of periodontitis than the normal salivation group (p < 0.05). The hyposalivation group also had a lower number of teeth present and a lower mean MNA score than the normal salivation group (p < 0.05). Logistic regression analysis showed that hyposalivation in both dentate and edentulous subjects was significantly associated with tasting, speaking, swallowing and chewing., Conclusion: This study suggested that hyposalivation is a risk factor not only for dental caries and periodontal disease but also for taste disturbances, speaking problems, swallowing problems, poor chewing ability and malnutrition. Monitoring salivary flow is an important measure in the care of older people.

Expression quantitative trait locus (eQTL) analysis is rapidly moving from a cutting-edge concept in genomics to a mature area of investigation, with important connections to genome-wide association studies for human disease, pharmacogenomics and toxicogenomics. Despite the importance of the topic, many investigators must develop their own code or use tools not specifically suited for eQTL analysis. Convenient computational tools are becoming available, but they are not widely publicized, and investigators who are interested in discovery or eQTL, or in using them to interpret genome-wide association study results may have difficulty navigating the available resources. The purpose of this review is to help investigators find appropriate programs for eQTL analysis and interpretation.

Aim: The main objective of this study was to investigate the prevalence of taste hyposensitivity and the relationships between sex, oral health status, and eating habits with taste hyposensitivity in Japanese senior high school students., Methods: Oral examinations, sweet and salt whole-mouth taste tests, and a questionnaire about eating habits were conducted on 234 senior high school students. Factors affecting taste hyposensitivity were investigated using a multivariate analysis., Results: Sweet-taste hyposensitivity was observed in 7.3% of the students, and salt-taste hyposensitivity in 22.2%. Approximately 3% of the students had both sweet- and salt-taste hyposensitivity, and 22.6% had either sweet- or salt-taste hyposensitivity. In total, 26% had a taste hyposensitivity. There were significant relationships between the intake of instant noodles with sweet-taste hyposensitivity, and the intake of vegetables or isotonic drinks with salt-taste hyposensitivity., Conclusions: There was a significant association between eating habits and taste hyposensitivity in Japanese senior high school students. Taste tests would be a helpful adjunct for students to recognize variations in taste sensitivity, and a questionnaire about their eating habits might provide an effective self-review of their eating habits, and therefore, provide motivation to change., (© 2011 Blackwell Publishing Asia Pty Ltd.)

Mouse models play a crucial role in the study of human behavioral traits and diseases. Variation of gene expression in brain may play a critical role in behavioral phenotypes, and thus it is of great importance to understand regulation of transcription in mouse brain. In this study, we analyzed the role of two important factors influencing steady-state transcriptional variation in mouse brain. First we considered the effect of assessing whole brain vs. discrete regions of the brain. Second, we investigated the genetic basis of strain effects on gene expression. We examined the transcriptome of three brain regions using Affymetrix expression arrays: whole brain, forebrain, and hindbrain in adult mice from two common inbred strains (C57BL/6J vs. NOD/ShiLtJ) with eight replicates for each brain region and strain combination. We observed significant differences between the transcriptomes of forebrain and hindbrain. In contrast, the transcriptomes of whole brain and forebrain were very similar. Using 4.3 million single-nucleotide polymorphisms identified through whole-genome sequencing of C57BL/6J and NOD/ShiLtJ strains, we investigated the relationship between strain effect in gene expression and DNA sequence similarity. We found that cis-regulatory effects play an important role in gene expression differences between strains and that the cis-regulatory elements are more often located in 5' and/or 3' transcript boundaries, with no apparent preference on either 5' or 3' ends.

Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots., Availability and Implementation: seeQTL is freely available for non-commercial use at http://www.bios.unc.edu/research/genomic&#95;software/seeQTL/., Contact: fred&#95;wright@unc.edu; kxia@bios.unc.edu, Supplementary Information: Supplementary data are available at Bioinformatics online.

We introduce the Interactive Decision Committee method for classification when high-dimensional feature variables are grouped into feature categories. The proposed method uses the interactive relationships among feature categories to build base classifiers which are combined using decision committees. A two-stage or a single-stage 5-fold cross-validation technique is utilized to decide the total number of base classifiers to be combined. The proposed procedure is useful for classifying biochemicals on the basis of toxicity activity, where the feature space consists of chemical descriptors and the responses are binary indicators of toxicity activity. Each descriptor belongs to at least one descriptor category. The support vector machine, the random forests, and the tree-based AdaBoost algorithms are utilized as classifier inducers. Forward selection is used to select the best combinations of the base classifiers given the number of base classifiers. Simulation studies demonstrate that the proposed method outperforms a single large, unaggregated classifier in the presence of interactive feature category information. We applied the proposed method to two toxicity data sets associated with chemical compounds. For these data sets, the proposed method improved classification performance for the majority of outcomes compared to a single large, unaggregated classifier.

Objective: The objective of this study was to investigate clinical oral health status relationships that affect quality of life (using the 12-item General Oral Health Assessment Index (GOHAI)) and self-rated oral health in a community of Japanese residents., Methods: 459 residents of Yokote City, Japan aged 40-55 years had oral health examinations and completed self-administered questionnaires collecting data on age, gender, GOHAI items and self-rated oral health. Linear regression analysis was performed with GOHAI or self-rated oral health as a dependent variable and gender, age and indicators of oral health status as independent variables., Results: The GOHAI indicated 42.7% of subjects were concerned about the appearance of their teeth, 30.1% were worried about teeth problems and 27.5% concerned about sensitive teeth. Analyses showed that gender, decayed teeth, oral dryness and missing teeth were significantly associated with variation in GOHAI scores, and that gender, decayed teeth, oral dryness and oral hygiene were significantly associated with variation in self-rated oral health., Conclusion: This study revealed that in this sample of Japanese adults aged 40-55 years, decayed teeth and oral dryness affected both GOHAI and self-rated oral health, whereas missing teeth affected GOHAI and oral hygiene affected self-rated oral health. Subjects did not recognise periodontal disease as a quality of life impacting condition or as a health problem.

Ric-8A (resistance to inhibitors of cholinesterase 8A) and Ric-8B are guanine nucleotide exchange factors that enhance different heterotrimeric guanine nucleotide-binding protein (G protein) signaling pathways by unknown mechanisms. Because transgenic disruption of Ric-8A or Ric-8B in mice caused early embryonic lethality, we derived viable Ric-8A- or Ric-8B-deleted embryonic stem (ES) cell lines from blastocysts of these mice. We observed pleiotropic G protein signaling defects in Ric-8A(-/-) ES cells, which resulted from reduced steady-state amounts of Gα(i), Gα(q), and Gα(13) proteins to <5% of those of wild-type cells. The amounts of Gα(s) and total Gβ protein were partially reduced in Ric-8A(-/-) cells compared to those in wild-type cells, and only the amount of Gα(s) was reduced substantially in Ric-8B(-/-) cells. The abundances of mRNAs encoding the G protein α subunits were largely unchanged by loss of Ric-8A or Ric-8B. The plasma membrane residence of G proteins persisted in the absence of Ric-8 but was markedly reduced compared to that in wild-type cells. Endogenous Gα(i) and Gα(q) were efficiently translated in Ric-8A(-/-) cells but integrated into endomembranes poorly; however, the reduced amounts of G protein α subunits that reached the membrane still bound to nascent Gβγ. Finally, Gα(i), Gα(q), and Gβ(1) proteins exhibited accelerated rates of degradation in Ric-8A(-/-) cells compared to those in wild-type cells. Together, these data suggest that Ric-8 proteins are molecular chaperones required for the initial association of nascent Gα subunits with cellular membranes.

Background: There is a possibility that genuine halitosis patients' anxiety do not recover after oral malodor treatment due to their social anxiety disorder. The objective of this study was to investigate the influence of social anxiety disorder on the level of anxiety in genuine halitosis patients before and after treatment for oral malodor., Methods: The subjects were 262 genuine halitosis patients who visited the Fresh Breath Clinic from March, 2008 to October, 2009. The subjects who had score 2 or higher by the organoleptic test were diagnosed as genuine halitosis patients. Gas chromatography (GC) was conducted before and after oral malodor treatment for the oral malodor measurement. Based on their risk of social anxiety disorder, subjects were divided into low- and high-risk groups using the Liebowitz Social Anxiety Scale (LSAS). The questions related to oral malodor and the clinical oral examination were both conducted before oral malodor treatment. The level of anxiety before and after oral malodor treatment was evaluated using the Visual Analogue Scale of Anxiety (VAAS)., Results: More than 20% of subjects had a score of 60 or more on the LSAS (high LSAS group). The mean age and the percentage of females were significantly higher in the high LSAS group compared to the low LSAS group. The high LSAS group was more likely to have problems associated with oral malodor and to adopt measures against oral malodor compared to the low LSAS group. The mean concentrations of H2S and CH3SH by GC significantly decreased after the oral malodor treatment in both LSAS groups. VAAS scores also significantly decreased after treatment in both LSAS groups. The logistic regression analysis indicated that the high LSAS group had a 2.28 times higher risk of having a post-VAAS score of 50 or more compared to the low LSAS group., Conclusions: This study revealed that genuine halitosis patients with a strong trait of social anxiety disorder have difficulty overcoming their anxiety about oral malodor. Oral malodor treatment of genuine halitosis patients requires not only regular oral malodor treatment but also attention to social anxiety disorder.

Background: Sporadic amyotrophic lateral sclerosis (sALS) is a motor neuron disease with poorly understood etiology. Results of gene expression profiling studies of whole blood from ALS patients have not been validated and are difficult to relate to ALS pathogenesis because gene expression profiles depend on the relative abundance of the different cell types present in whole blood. We conducted microarray analyses using Agilent Human Whole Genome 4 × 44k Arrays on a more homogeneous cell population, namely purified peripheral blood lymphocytes (PBLs), from ALS patients and healthy controls to identify molecular signatures possibly relevant to ALS pathogenesis., Methods: Differentially expressed genes were determined by LIMMA (Linear Models for MicroArray) and SAM (Significance Analysis of Microarrays) analyses. The SAFE (Significance Analysis of Function and Expression) procedure was used to identify molecular pathway perturbations. Proteasome inhibition assays were conducted on cultured peripheral blood mononuclear cells (PBMCs) from ALS patients to confirm alteration of the Ubiquitin/Proteasome System (UPS)., Results: For the first time, using SAFE in a global gene ontology analysis (gene set size 5-100), we show significant perturbation of the KEGG (Kyoto Encyclopedia of Genes and Genomes) ALS pathway of motor neuron degeneration in PBLs from ALS patients. This was the only KEGG disease pathway significantly upregulated among 25, and contributing genes, including SOD1, represented 54% of the encoded proteins or protein complexes of the KEGG ALS pathway. Further SAFE analysis, including gene set sizes >100, showed that only neurodegenerative diseases (4 out of 34 disease pathways) including ALS were significantly upregulated. Changes in UBR2 expression correlated inversely with time since onset of disease and directly with ALSFRS-R, implying that UBR2 was increased early in the course of ALS. Cultured PBMCs from ALS patients accumulated more ubiquitinated proteins than PBMCs from healthy controls in a serum-dependent manner confirming changes in this pathway., Conclusions: Our study indicates that PBLs from sALS patients are strong responders to systemic signals or local signals acquired by cell trafficking, representing changes in gene expression similar to those present in brain and spinal cord of sALS patients. PBLs may provide a useful means to study ALS pathogenesis.

Motivation: A number of penalization and shrinkage approaches have been proposed for the analysis of microarray gene expression data. Similar techniques are now routinely applied to RNA sequence transcriptional count data, although the value of such shrinkage has not been conclusively established. If penalization is desired, the explicit modeling of mean-variance relationships provides a flexible testing regimen that 'borrows' information across genes, while easily incorporating design effects and additional covariates., Results: We describe BBSeq, which incorporates two approaches: (i) a simple beta-binomial generalized linear model, which has not been extensively tested for RNA-Seq data and (ii) an extension of an expression mean-variance modeling approach to RNA-Seq data, involving modeling of the overdispersion as a function of the mean. Our approaches are flexible, allowing for general handling of discrete experimental factors and continuous covariates. We report comparisons with other alternate methods to handle RNA-Seq data. Although penalized methods have advantages for very small sample sizes, the beta-binomial generalized linear model, combined with simple outlier detection and testing approaches, appears to have favorable characteristics in power and flexibility., Availability: An R package containing examples and sample datasets is available at http://www.bios.unc.edu/research/genomic&#95;software/BBSeq, Contact: yzhou@bios.unc.edu; fwright@bios.unc.edu, Supplementary Information: Supplementary data are available at Bioinformatics online.

Genetic studies of lung disease in cystic fibrosis (CF) are hampered by the lack of a severity measure that accounts for chronic disease progression and mortality attrition. Further, combining analyses across studies requires common phenotypes that are robust to study design and patient ascertainment. Using data from the North American Cystic Fibrosis Modifier Consortium (Canadian Consortium for CF Genetic Studies, Johns Hopkins University CF Twin and Sibling Study, and University of North Carolina/Case Western Reserve University Gene Modifier Study), the authors calculated age-specific CF percentile values of FEV1 which were adjusted for CF age-specific mortality data. The phenotype was computed for 2,061 patients representing the Canadian CF population, 1,137 extreme phenotype patients in the UNC/Case Western study, and 1,323 patients from multiple CF sib families in the CF Twin and Sibling Study. Despite differences in ascertainment and median age, our phenotype score was distributed in all three samples in a manner consistent with ascertainment differences, reflecting the lung disease severity of each individual in the underlying population. The new phenotype score was highly correlated with the previously recommended complex phenotype, but the new phenotype is more robust for shorter follow-up and for extreme ages. A disease progression and mortality-adjusted phenotype reduces the need for stratification or additional covariates, increasing statistical power, and avoiding possible distortions. This approach will facilitate large-scale genetic and environmental epidemiological studies which will provide targeted therapeutic pathways for the clinical benefit of patients with CF., (Copyright © 2011 Wiley-Liss, Inc.)

In genome-wide association studies, population stratification is recognized as producing inflated type I error due to the inflation of test statistics. Principal component-based methods applied to genotypes provide information about population structure, and have been widely used to control for stratification. Here we explore the precise relationship between genotype principal components and inflation of association test statistics, thereby drawing a connection between principal component-based stratification control and the alternative approach of genomic control. Our results provide an inherent justification for the use of principal components, but call into question the popular practice of selecting principal components based on significance of eigenvalues alone. We propose a new approach, called EigenCorr, which selects principal components based on both their eigenvalues and their correlation with the (disease) phenotype. Our approach tends to select fewer principal components for stratification control than does testing of eigenvalues alone, providing substantial computational savings and improvements in power. Analyses of simulated and real data demonstrate the usefulness of the proposed approach., (© 2010, The International Biometric Society.)

MicroRNAs are short, non-coding RNA sequences that regulate genes at the post-transcriptional level and have been shown to be important in development, tissue differentiation, and disease. Limited attention has been given to the natural variation in miRNA expression across genetically diverse populations even though it is well established that genetic polymorphisms can have a profound effect on mRNA levels. Expression level of 577 miRNAs in the livers of 70 strains of inbred mice was assessed, and we found that miRNA expression is highly stable across different strains. Globally, the expression of miRNA target transcripts does not correlate with miRNA expression, primarily due to the low variance of miRNA but high variance of mRNA expression across strains. Our results show that there is little genetic effect on the baseline miRNA levels in murine liver. The stability of mouse liver miRNA expression in a genetically diverse population suggests that treatment-induced disruptions in liver miRNA expression, a phenomenon established for a large number of toxicants, may indicate an important mechanism for the disturbance of normal liver function, and may prove to be a useful genetic background-independent biomarker of toxicant effect., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Objective: The Australian population is ageing, and a growing proportion of elderly Australians are now living in residential aged care facilities (RACFs). These residents are commonly dependent on others for their daily oral hygiene care and often display high levels of plaque and calculus. With declining edentulism rates, periodontal disease is becoming more prevalent in this population. The aim of this study was to investigate the ability of a dental hygienist to undertake a dental examination for residents of aged care facilities, devise a periodontal and preventive treatment plan and refer patients appropriately to a dentist., Methods: A total of 510 residents from 31 Victorian RACFs were examined, with 275 dentate residents included in this study. Between May 2005 and June 2006, residents were examined by a single experienced dental epidemiologist and one of four dental hygienists using a plane mouth mirror and periodontal probe., Results: A total of 510 residents from 31 RACFs had a dental examination from a dentist and one of four dental hygienists. The treatment needs of residents examined were high, with nearly all of the 275 dentate residents requiring preventive and periodontal treatment, and three-quarters requiring referral to a dentist for treatment. There was excellent agreement between the dentist and hygienists regarding the decision to refer residents to a dentist for treatment, with high sensitivity (99.6%) and specificity (82.9%). Only 8.0% of residents were referred by a hygienist to a dentist when the dentist considered that no referral was required., Conclusions: Dental hygienists have the skills and knowledge necessary for undertaking a dental examination for residents, correctly identifying the majority of residents who require a referral to a dentist. They are capable of formulating appropriate dental hygiene treatment plans for residents of aged care facilities. It is recommended that there should be greater utilization of hygienists in the provision of dental care to residents of aged care facilities, as a safe, efficient and effective use of health resources., (© 2011 John Wiley & Sons A/S.)