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DNA methylation (DNAm) is a dynamic, age-dependent, epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergy. One method to study the role of DNAm is the epigenetic clock – an algorithm that uses DNAm levels at select age informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such asthma and allergic diseases which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma and in utero and early life exposures (e.g., smoking, diet, and drugs) that result in methylation changes.

Identifying disease‐associated changes in DNA methylation can help us gain a better understanding of disease etiology. Bisulfite sequencing allows the generation of high‐throughput methylation profiles at single‐base resolution of DNA. However, optimally modeling and analyzing these sparse and discrete sequencing data is still very challenging due to variable read depth, missing data patterns, long‐range correlations, data errors, and confounding from cell type mixtures. We propose a regression‐based hierarchical model that allows covariate effects to vary smoothly along genomic positions and we have built a specialized EM algorithm, which explicitly allows for experimental errors and cell type mixtures, to make inference about smooth covariate effects in the model. Simulations show that the proposed method provides accurate estimates of covariate effects and captures the major underlying methylation patterns with excellent power. We also apply our method to analyze data from rheumatoid arthritis patients and controls. The method has been implemented in R package SOMNiBUS.

Clonal complex 398 (CC398) livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been reported worldwide in a variety of food-animal species. Although CC398 is synonymous with LA-MRSA, community-associated MRSA (CA-MRSA) variants have emerged, including the Panton-Valentine leukocidin (PVL)-positive ST398-V and ST398 single-locus variant ST1232-V, and the PVL-negative ST398-V clones. Using comparative genomic analysis, we determined whether ten CC398 MRSA bacteraemia episodes recently identified in Australia were due to LA-MRSA or CA-MRSA CC398. Isolates were sourced from the Australian Group on Antimicrobial Resistance S. aureus surveillance programme and episodes occurred across Australia. Whole-genome sequencing (WGS) and phylogenetic comparison of the ten CC398 bacteraemia isolates with previously published CC398 MRSA whole-genome sequences identified that the Australian CC398 isolates were closely related to the human-associated II-GOI clade and the livestock-associated IIa clade. The identified CC398 MRSA clones were: PVL-positive ST1232-V (5C25), PVL-negative community-associated ST398-V (5C25) and livestock-associated ST398-V (5C25). Our findings demonstrate the importance of using WGS and comparing the sequences with international sequences to distinguish between CC398 CA-MRSA and LA-MRSA and to determine the isolates' origin. Furthermore, our findings suggest that CC398 CA-MRSA has become established in the Australian community and that ST398-V (5C25) LA-MRSA is now widespread in Australian piggeries. Our study emphasises the need for national One Health antimicrobial resistance surveillance programmes to assist in monitoring the ongoing epidemiology of MRSA and other clinically significant antimicrobial-resistant organisms.

Rationale Sleep duration is critical to growth, learning, and immune function development in infancy. Strategies to ensure that national recommendations for sleep duration in infants are met require knowledge of perinatal factors that affect infant sleep. Objectives To investigate the mechanistic pathways linking maternal education and infant sleep. Methods An observational study was conducted on 619 infants whose mothers were enrolled at the Edmonton site of the CHILD birth cohort. Infant sleep duration at three months was assessed using the Brief Infant Sleep Questionnaire. Maternal education was collected via maternal report. Prenatal and postnatal depression scores were obtained from the 20-item Center for Epidemiologic Studies Depression Scale (CES-D). Birth records and maternal report were the source of covariate measures. Mediation analysis (PROCESS v3.0) was used to examine the indirect effects of maternal education on infant sleep duration mediated through prenatal depression and birth mode. Measurements and main results At three months of age, infants slept on average 14.1 h. Lower maternal education and prenatal depression were associated with significantly shorter infant sleep duration. Emergency cesarean section birth was associated with 1-hour shorter sleep duration at three months compared to vaginal birth [without intrapartum antibiotic prophylaxis] (β: −0.99 h; 95% CI: −1.51, −0.48). Thirty percent of the effect of lower maternal education on infant total sleep duration was mediated sequentially through prenatal depression and birth mode (Total Indirect Effects: −0.12, 95% CI: −0.22, −0.03, p Conclusions Prenatal depression and birth mode sequentially mediate the effect of maternal education on infant sleep duration.

_To the Editor:_ Previously, we identified the HLA region as a risk factor forpeanut allergy (PA); this observation is supported further by 2 independent genome-wide association studies (GWASs). The HLA class II genes (including HLA-DR, HLA-DQ, and HLADP) encode molecules involved in presentation of extracellular antigens, such as peanut allergens, to T lymphocytes, which in turn mediates B-cell antibody production.We used the Canadian Peanut Allergy Registry (CanPAR) and the Busselton Health Study to conduct the largest GWAS for PA to date. Here we report analysis of the HLA region and a meta-analysis with data from 6 additional studies, which confirms and narrows the region of interest to HLA-DQB1 and establishes independence from asthma loci. [...]

Background Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously, PA loci were identified in filaggrin (FLG) and HLA in candidate gene studies, and loci in HLA were identified in a genome-wide association study and meta-analysis. Objective We sought to investigate genetic susceptibility to PA. Methods Eight hundred fifty cases and 926 hyper-control subjects and more than 7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were analyzed in a genome-wide association study to identify susceptibility variants for PA in the Canadian population. A meta-analysis of 2 phenotypes (PA and food allergy) was conducted by using 7 studies from the Canadian, American (n = 2), Australian, German, and Dutch (n = 2) populations. Results An SNP near integrin α6 (ITGA6) reached genome-wide significance with PA ( P = 1.80 × 10 −8 ), whereas SNPs associated with Src kinase–associated phosphoprotein 1 (SKAP1) , matrix metallopeptidase 12 (MMP12)/MMP13 , catenin α3 (CTNNA3) , rho GTPase–activating protein 24 (ARHGAP24) , angiopoietin 4 (ANGPT4) , chromosome 11 open reading frame (C11orf30/EMSY) , and exocyst complex component 4 (EXOC4) reached a threshold suggestive of association ( P ≤ 1.49 × 10 −6 ). In the meta-analysis of PA, loci in or near ITGA6 , ANGPT4 , MMP12/MMP13 , C11orf30 , and EXOC4 were significant ( P ≤ 1.49 × 10 −6 ). When a phenotype of any food allergy was used for meta-analysis, the C11orf30 locus reached genome-wide significance ( P = 7.50 × 10 −11 ), whereas SNPs associated with ITGA6 , ANGPT4 , MMP12/MMP13 , and EXOC4 and additional C11orf30 SNPs were suggestive ( P ≤ 1.49 × 10 −6 ). Functional annotation indicated that SKAP1 regulates expression of CBX1 , which colocalizes with the EMSY protein coded by C11orf30. Conclusion This study identifies multiple novel loci as risk factors for PA and food allergy and establishes C11orf30 as a risk locus for both PA and food allergy. Multiple genes ( C11orf30 / EMSY , SKAP1 , and CTNNA3 ) identified by this study are involved in epigenetic regulation of gene expression.

A systematic review of pharmacogenomic studies capturing adverse drug reactions (ADRs) related to asthma medications was undertaken, and a survey of Pharmacogenomics in Childhood Asthma (PiCA) consortia members was conducted. Studies were eligible if genetic polymorphisms were compared with suspected ADR(s) in a patient with asthma, as either a primary or secondary outcome. Five studies met the inclusion criteria. The ADRs and polymorphisms identified were change in lung function tests (rs1042713), adrenal suppression (rs591118), and decreased bone mineral density (rs6461639) and accretion (rs9896933, rs2074439). Two of these polymorphisms were replicated within the paper, but none had external replication. Priorities from PiCA consortia members (representing 15 institution in eight countries) for future studies were tachycardia (SABA/LABA), adrenal suppression/crisis and growth suppression (corticosteroids), sleep/behaviour disturbances (leukotriene receptor antagonists), and nausea and vomiting (theophylline). Future pharmacogenomic studies in asthma should collect relevant ADR data as well as markers of efficacy.

A systematic review of pharmacogenomic studies capturing adverse drug reactions (ADRs) related to asthma medications was undertaken, and a survey of Pharmacogenomics in Childhood Asthma (PiCA) consortia members was conducted. Studies were eligible if genetic polymorphisms were compared with suspected ADR(s) in a patient with asthma, as either a primary or secondary outcome. Five studies met the inclusion criteria. The ADRs and polymorphisms identified were change in lung function tests (rs1042713), adrenal suppression (rs591118), and decreased bone mineral density (rs6461639) and accretion (rs9896933, rs2074439). Two of these polymorphisms were replicated within the paper, but none had external replication. Priorities from PiCA consortia members (representing 15 institution in eight countries) for future studies were tachycardia (SABA/LABA), adrenal suppression/crisis and growth suppression (corticosteroids), sleep/behaviour disturbances (leukotriene receptor antagonists), and nausea and vomiting (theophylline). Future pharmacogenomic studies in asthma should collect relevant ADR data as well as markers of efficacy.

Background The atopic march describes the progression from atopic dermatitis during infancy to asthma and allergic rhinitis in later childhood. In a Canadian birth cohort we investigated whether concomitant allergic sensitization enhances subsequent development of these allergic diseases at age 3 years. Methods Children completed skin prick testing at age 1 year. Children were considered sensitized if they produced a wheal 2 mm or larger than that elicited by the negative control to any of 10 inhalant or food allergens. Children were also assessed for atopic dermatitis by using the diagnostic criteria of the UK Working Party. At age 3 years, children were assessed for asthma, allergic rhinitis, food allergy, and atopic dermatitis. Data from 2311 children were available. Results Atopic dermatitis without allergic sensitization was not associated with an increased risk of asthma at age 3 years after adjusting for common confounders (relative risk [RR], 0.46; 95% CI, 0.11-1.93). Conversely, atopic dermatitis with allergic sensitization increased the risk of asthma more than 7-fold (RR, 7.04; 95% CI, 4.13-11.99). Atopic dermatitis and allergic sensitization had significant interactions on both the additive (relative excess risk due to interaction, 5.06; 95% CI, 1.33-11.04) and multiplicative (ratio of RRs, 5.80; 95% CI, 1.20-27.83) scales in association with asthma risk. There was also a positive additive interaction between atopic dermatitis and allergic sensitization in their effects on food allergy risk (relative excess risk due to interaction, 15.11; 95% CI, 4.19-35.36). Conclusions Atopic dermatitis without concomitant allergic sensitization was not associated with an increased risk of asthma. In combination, atopic dermatitis and allergic sensitization had strong interactive effects on both asthma and food allergy risk at age 3 years.

Objective To determine whether different modes of infant feeding are associated with childhood asthma, including differentiating between direct breastfeeding and expressed breast milk. Study design We studied 3296 children in the Canadian Healthy Infant Longitudinal Development birth cohort. The primary exposure was infant feeding mode at 3 months, reported by mothers and categorized as direct breastfeeding only, breastfeeding with some expressed breast milk, breast milk and formula, or formula only. The primary outcome was asthma at 3 years of age, diagnosed by trained healthcare professionals. Results At 3 months of age, the distribution of feeding modes was 27% direct breastfeeding, 32% breastfeeding with some expressed breast milk, 26% breast milk and formula, and 15% formula only. At 3 years of age, 12% of children were diagnosed with possible or probable asthma. Compared with direct breastfeeding, any other mode of infant feeding was associated with an increased risk of asthma. These associations persisted after adjusting for maternal asthma, ethnicity, method of birth, infant sex, gestational age, and daycare attendance (some expressed breast milk: aOR, 1.64, 95% CI, 1.12-2.39; breast milk and formula, aOR, 1.73, 95% CI, 1.17-2.57; formula only: aOR, 2.14, 95% CI, 1.37-3.35). Results were similar after further adjustment for total breastfeeding duration and respiratory infections. Conclusions Modes of infant feeding are associated with asthma development. Direct breastfeeding is most protective compared with formula feeding; indirect breast milk confers intermediate protection. Policies that facilitate and promote direct breastfeeding could have impact on the primary prevention of asthma.

Respiratory diseases are the most frequent chronic illnesses in babies and children. Although a vigorous innate immune system is critical for maintaining lung health, a balanced response is essential to minimize damaging inflammation. We investigated the functional and clinical impact of human genetic variants in the promoter of NFKBIA, which encodes IκBα, the major negative regulator of NF-κB. In this study, we quantified the functional impact of NFKBIA promoter polymorphisms (rs3138053, rs2233406, and rs2233409) on promoter-driven protein expression, allele-specific and total NFKBIA mRNA expression, IκBα protein expression, and TLR responsiveness; mapped innate immune regulatory networks active during respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia; and genotyped and analyzed independent cohorts of children with respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia. Genetic variants in the promoter of NFKBIA influenced NFKBIA gene expression, IκBα protein expression, and TLR-mediated inflammatory responses. Using a systems biology approach, we demonstrated that NFKBIA/IκBα is a central hub in transcriptional responses of prevalent childhood lung diseases, including respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia. Finally, by examining independent pediatric lung disease cohorts, we established that this immunologically relevant genetic variation in the promoter of NFKBIA is associated with differential susceptibility to severe bronchiolitis following infection with respiratory syncytial virus, airway hyperresponsiveness, and severe bronchopulmonary dysplasia. These data highlight the importance of negative innate immune regulators, such as NFKBIA, in pediatric lung disease and begin to unravel common aspects in the genetic predisposition to bronchopulmonary dysplasia, bronchiolitis, and childhood asthma.

Background IgE is both a marker and mediator of allergic inflammation. Despite reported differences in serum total IgE levels by race-ethnicity, African American and Latino subjects have not been well represented in genetic studies of total IgE. Objective We sought to identify the genetic predictors of serum total IgE levels. Methods We used genome-wide association data from 4292 subjects (2469 African Americans, 1564 European Americans, and 259 Latinos) in the EVE Asthma Genetics Consortium. Tests for association were performed within each cohort by race-ethnic group (ie, African American, Latino, and European American) and asthma status. The resulting P values were meta-analyzed, accounting for sample size and direction of effect. Top single nucleotide polymorphism associations from the meta-analysis were reassessed in 6 additional cohorts comprising 5767 subjects. Results We identified 10 unique regions in which the combined association statistic was associated with total serum IgE levels ( P −6 ) and the minor allele frequency was 5% or greater in 2 or more population groups. Variant rs9469220, corresponding to HLA-DQB1 , was the single nucleotide polymorphism most significantly associated with serum total IgE levels when assessed in both the replication cohorts and the discovery and replication sets combined ( P = .007 and 2.45 × 10 −7 , respectively). In addition, findings from earlier genome-wide association studies were also validated in the current meta-analysis. Conclusion This meta-analysis independently identified a variant near HLA-DQB1 as a predictor of total serum IgE levels in multiple race-ethnic groups. This study also extends and confirms the findings of earlier genome-wide association analyses in African American and Latino subjects.

BACKGROUND: Both asthma and obesity are complex disorders that are influenced by environmental and genetic factors. Shared genetic factors between asthma and obesity have been proposed to partly explain epidemiological findings of co-morbidity between these conditions. OBJECTIVE: To identify genetic variants that are associated with body mass index (BMI) in asthmatic children and adults, and to evaluate if there are differences between the genetics of BMI in asthmatics and healthy individuals. METHODS: In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWA data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. RESULTS: We report associations between several DENND1B variants (P = 2.2 × 10(-7) for rs4915551) on chromosome 1q31 and BMI from a meta-analysis of GWAS data using 2691 asthmatic children (screening data). The top DENND1B single nucleotide polymorphisms (SNPs) were next evaluated in seven independent replication data sets comprising 2014 asthmatics, and rs4915551 was nominally replicated (P > 0.05) in two of the seven studies and of borderline significance in one (P = 0.059). However, strong evidence of effect heterogeneity was observed and overall, the association between rs4915551 and BMI was not significant in the total replication data set, P = 0.71. Using a random effects model, BMI was overall estimated to increase by 0.30 kg/m(2) (P = 0.01 for combined screening and replication data sets, N = 4705) per additional G allele of this DENND1B SNP. FTO was confirmed as an important gene for adult and childhood BMI regardless of asthma status. CONCLUSIONS AND CLINICAL RELEVANCE: DENND1B was recently identified as an asthma susceptibility gene in a GWAS on children, and here, we find evidence that DENND1B variants may also be associated with BMI in asthmatic children. However, the association was overall not replicated in the independent data sets and the heterogeneous effect of DENND1B points to complex associations with the studied diseases that deserve further study.

Peanut allergy (PA) is a common and serious food allergy and its prevalence has increased in the past decade. Although there is strong evidence of inheritance, the genetic causes of this disease are not well understood. Previously, a large-scale genome-wide association study described an association between human leukocyte antigen (HLA)-DQB1 and asthma; the aim of this study was to evaluate the association between HLA-DQB1 and PA. Genotypic and allelic profiles were established for 311 Caucasian members of a well-described Canadian group of children with PA and 226 Caucasian controls. Firth's logistic regression analyses showed associations between HLA-DQB1 alleles and PA for DQB1*02 (P=1.1 × 10(-8), odds ratio (OR)=0.09 (CI=0.03-0.23)) and DQB1*06:03P alleles (P=2.1 × 10(-2), OR=2.82 (CI=1.48-5.45)). This study of HLA in PA demonstrates specific association between two allelic groups of the HLA-DQB1 gene (DQB1*02 and DQB1*06:03P) and PA, highlighting its possible role in the development of this disease.

Our gut microbiota provide a number of important functions, one of which is the metabolism of dietary fiber and other macronutrients that are undigested by the host. The main products of this fermentation process are short-chain fatty acids (SCFAs) and other intermediate metabolites including lactate and succinate. Production of these metabolites is dependent on diet and gut microbiota composition. There is increasing evidence for the role of SCFAs in host physiology and metabolic processes as well as chronic inflammatory conditions such as allergic disease and obesity. We aimed to investigate differences in fecal SCFAs and intermediate metabolites in 163 infants at 3–5 months of age according to breastfeeding status. Compared to no exposure to human milk at time of fecal sample collection, exclusive breastfeeding was associated with lower absolute concentrations of total SCFAs, acetate, butyrate, propionate, valerate, isobutyrate, and isovalerate, yet higher concentrations of lactate. Further, the relative proportion of acetate was higher with exclusive breastfeeding. Compared to non-breastfed infants, those exclusively breastfed were four times more likely (aOR 4.50, 95% CI 1.58–12.82) to have a higher proportion of acetate relative to other SCFAs in their gut. This association was independent of birth mode, intrapartum antibiotics, infant sex, age, recruitment site, and maternal BMI or socioeconomic status. Our study confirms that breastfeeding strongly influences the composition of fecal microbial metabolites in infancy.

Background: Genetic variation may partly explain heterogeneity in response to asthma treatment . Recently, the P harmacogenomics i n C hildhood A sthma (PiCA) consortium was initiated to perform large-scale pharmacogenomics studies. Aims: To describe the characteristics of the asthmatic children currently included in PiCA and to assess treatment response definitions within this growing consortium. Methods: An online survey including questions about data collection, patient characteristics and outcome phenotypes was send to the 20 studies included in the PiCA consortium. Results: In total, 14,634 children/young adults (up to 25 years) from 11 different countries are enrolled in the PiCA consortium. Preliminary analysis of patients showed that 60% of the patients are male. PiCA is ethnically diverse: 47% Caucasians, 25% Latinos, 14% Asians, 9% African-Americans, 2% have mixed/other-ethnicity and 3% is unknown. PiCA currently includes data of 2,056 severe asthmatics. Furthermore, PiCA has data of 8,907 short acting β 2 -adrenergic agonist (SABA) users, 7,908 ICS users, 2,054 leukotriene modifier (LTM) users and 1,543 users of long acting β 2 -adrenergic agonists (LABA). Ninety-five percent of the studies have information regarding asthma exacerbations and lung function measurements and 80% have data on asthma symptoms. Discussion: The children within the PiCA consortium are a reflection of the global heterogeneous pediatric asthma population. Different outcome measures reflect different dimensions of asthma. By classifying three commonly used outcome measures using data that are available within the PiCA consortium, we will be able to study distinct response phenotypes in relation to genetics and clinical factors.

New treatments are needed to improve the health of people with cystic fibrosis (CF). Reducing lung-damaging inflammation is likely to be beneficial, but specific anti-inflammatory targets have not been identified. By combining cellular immunology with a population-based genetic modifier study, we examined TLR5 as an anti-inflammatory target and modifier gene in CF. Using two pairs of human CF and control airway epithelial cells, we demonstrated that the TLR5–flagellin interaction is a major mediator of inflammation following exposure to Pseudomonas aeruginosa. To validate TLR5 as an anti-inflammatory target, we analyzed the disease modifying effects of the TLR5 c.1174C>T single nucleotide polymorphism (rs5744168) in a large cohort of CF patients (n = 2219). rs5744168 encodes a premature stop codon and the T allele is associated with a 45.5–76.3% reduction in flagellin responsiveness (p < 0.0001). To test the hypothesis that reduced TLR5 responsiveness would be associated with improved health in CF patients, we examined the relationship between rs5744168 and two clinical phenotypes: lung function and body weight. Adults with CF carrying the TLR5 premature stop codon (CT or TT genotype) had a higher body mass index than did CF patients homozygous for the fully functional allele (CC genotype) (p = 0.044); however, similar improvements in lung function associated with the T allele were not statistically significant. Although follow-up studies are needed to confirm the impact of TLR5 on nutritional status, this translational research provides evidence that genetic variation in TLR5 resulting in reduced flagellin responsiveness is associated with improved health indicators in adults with CF.

Clonal mosaicism for large chromosomal anomalies (duplications, deletions and uniparental disomy) was detected using SNP microarray data from over 50,000 subjects recruited for genome-wide association studies. This detection method requires a relatively high frequency of cells (>5–10%) with the same abnormal karyotype (presumably of clonal origin) in the presence of normal cells. The frequency of detectable clonal mosaicism in peripheral blood is low (

Chronic obstructive pulmonary disease (COPD) is defined by the Global Initiative for Chronic Obstructive Lung Disease (GOLD) as a disease state characterized by airflow limitation that is not fully reversible (1). Cigarette smoking is the most important risk factor for the development of COPD. Although the dose-response relationship between cigarette smoking and pulmonary function is well-established, there is considerable variability in the reduction in FEV1 among smokers with similar smoking exposures (2, 3). The low percentage of variance in pulmonary function explained by smoking suggests that there could be genetic differences in susceptibility to the effects of cigarette smoking (4, 5). In addition to genetic factors, other environmental determinants such as indoor biomass smoke exposure can be important risk factors for COPD (6). A small percentage of COPD patients (estimated at 1-2%) inherit severe alpha-1 antitrypsin (AAT) deficiency, which proves that genetic factors can in-fluence COPD susceptibility. The discovery of AAT deficiency was a major factor in the development of the Protease-Antiprotease Hypothesis for COPD, which has been one of the prevailing models of disease pathogenesis for more than 40 years. With the substantial impact of AAT deficiency on our understanding of COPD pathogenesis, it was natural to hope that the identification of other COPD susceptibility genes would lead to similar novel insights into COPD. Until recently, however, progress in the identification of additional genetic risk factors for COPD has been slow. To facilitate the development of such research, a meeting of COPD genetics investigators was held on July 13-14,2010 in Boston. The goals of the meeting were: To review the current state of COPD genetics research; To discuss existing study populations for COPD genetics research throughout the world; To consider opportunities for collaborations between different COPD research groups through an International COPD Genetics Consortium; To recognize challenges in building COPD genetics collaborations and to discuss them openly; and, To develop a framework for future collaborative studies. Current status of COPD genetics research Many candidate gene association studies have been performed over the past 40 years, but the results have been largely inconsistent. These inconsistencies likely relate to a variety of methodological issues, including small sample sizes, variable definitions of case and control groups, failure to adjust for multiple statistical testing, and inadequate adjustments for population stratification and smoking exposure. Most of the studies describing COPD-associated polymorphisms were performed in White populations (7). A meta-analysis of 20 polymorphisms in 12 candidate genes involved in the protease-antiprotease balance and several an-tioxidant pathways showed that, after combining independent studies, many of these candidate genes had no association with COPD (8). Another factor likely impeding the progress of identifying COPD susceptibility genes is the lack of accurate phenotypic characterization of this complex and heterogeneous disease. Airflow limitation determined by spirometry has been the most common approach to classify and monitor the disease. Structural changes of the lung including emphysema and small airway obstruction are the primary processes that affect lung function (9), but they are not easily discernable with the simple spirometric measures commonly used for phe-notyping COPD. Recent advances in characterizing pathologic changes such as emphysema and remodeling of the small and large airways by quantitative analyses of image data from multidetector computed tomography (CT), together with physiological testing, have been helpful to differentiate COPD phenotypes (emphysema-predominant, airway-predominant, or mixed)(10). Study populations that have chest CT data may help to better identify COPD-associated genetic variations (11). Other potentially relevant COPD phenotypes, such as cachexia and low exercise capacity, have not been widely analyzed in COPD genetic studies. Perhaps the greatest problem in the candidate gene era of COPD genetic studies was improper candidate gene selection, which reflects our limited understanding of COPD pathogenesis. However, the application of genome-wide association studies (GWAS), which provide an unbiased and comprehensive search throughout the genome for common susceptibility loci, has changed the landscape of COPD genetics. Based on GWAS, three genetic loci have been unequivocally associated with COPD susceptibility, located on chromosome 4 near the HHIP gene, on chromosome 4 in the FAM13A gene, and on chromosome 15 in a block of genes which contains several components of the nicotinic acetyl-choline receptor as well as the IREB2 gene. In 2009, a series of studies provided convincing support for these three genetic loci in COPD susceptibility. Pillai and colleagues found genome-wide significant associations of the CHRNA3/CHRNA5/IREB2 region to COPD (12). DeMeo and colleagues performed gene expression studies of normal vs. COPD lung tissues followed by genetic association analysis of COPD (13), suggesting that at least one of the key COPD genetic determinants in the chromosome 15 GWAS region was IREB2. In the Framingham Heart Study (14), the HHIP region was associated with FEV1/FVC at genome-wide significance with replication of the effect on FEV1/FVC demonstrated in an independent sample drawn from the Family Heart Study, and this same region nearly reached genome-wide significance with COPD susceptibility in the Pillai paper (12). Recently, two papers published in Nature Genetics from large general population samples have provided strong support for the association of HHIP SNPs with FEV1/FVC (15, 16). One of these articles, from the CHARGE Consortium, also found evidence for association of FEV1/FVC with the FAM13A locus (15), which has been strongly associated with COPD susceptibility (17). Moreover, several case-control studies from other European populations have replicated these findings by confirming significant associations to the chromosome 15q25 locus (CHRNA3/CHRNA5/IREB2) (18, 19), chromosome 4q31 locus (HHIP) (20, 21), and chromosome 4q22 locus (FAM13 A) (22). Thus, the frustration of inconsistent genetic association results in COPD from the beginning of the last decade has been replaced by optimism regarding the likely importance of the IREB2/CHRNA3/CHRNA5, HHIP, and FAM13A loci in COPD susceptibility.

Cystic fibrosis (CF) is one of the most common life-shortening genetic disorders, and the CF transmembrane conductance regulator (CFTR) is the major causal gene. However, a substantial clinical variability among patients with identical CFTR genotypes suggests the presence of modifier genes. We tested the effect of four genes involved in Pseudomonas aeruginosa infection. Analysis of a primary cohort detected eight candidate polymorphisms that were genotyped in the secondary cohort of 1579 patients; lung function and age at first infection with P. aeruginosa were considered as the phenotypes. Both additive and codominant models were considered, adjusting for confounding variables but not for multiple comparisons. In the secondary cohort, heme oxygenase-1 (HMOX1) rs2071749 had the most significant effect on lung function in the pediatric group (P=0.01; P(corrected)=0.03), and complement factor 3 (C3) rs11569393 and HMOX1 rs2071746 in the adult groups (P=0.03 for both variants; P(corrected)=0.16, 0.09). No polymorphism of complement factor B (CFB) or toll-like receptor 4 (TLR4) had a significant modifying effect on lung function in either group. We have identified two genes that showed nominal association with disease severity among CF patients. However, because of the multiple comparisons made, further studies are required to confirm the interaction between these modifying genes and CFTR.

Summary Background Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48 201) for forced expiratory volume in 1 s (FEV 1 ) and the ratio of FEV 1 to forced vital capacity (FEV 1 /FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. Methods The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. Findings SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. Interpretation The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. Funding The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS.

BACKGROUND Severe anaphylactoid reactions to isosulfan blue dye requiring resuscitation are reported to occur in 1.1% of patients with breast carcinoma undergoing sentinel lymphadenectomy. In December 2001, the authors began administering a prophylactic regimen before dye injection to determine whether prophylaxis reduced the incidence of life-threatening reactions. METHODS All patients were mapped with technetium-99m–labeled sulfur colloid. Those also receiving isosulfan blue dye were administered a glucocorticoid, diphenhydramine, and famotidine intravenously just before or at induction of anesthesia. Adverse reactions at the time of surgery were analyzed. RESULTS Between December 2001 and July 2003, 1013 consecutive patients underwent sentinel lymphadenectomy for breast carcinoma. Six hundred sixty-seven patients (65.8%) received prophylaxis and isosulfan blue dye, 33 (3.3%) received prophylaxis but no dye, 12 (1.2%) received dye but no prophylaxis, and 301 (29.7%) received no prophylaxis or dye. Blue urticaria and facial edema were observed in 3 (0.5%) of 667 patients receiving prophylaxis and dye and in 1 (8.3%) of 12 patients receiving dye but no prophylaxis. There were no episodes of hypotension, and no patients required vasopressors, ventilatory support, or intensive care observation. Adverse reactions to agents other than blue dye were observed in 2 (0.3%) of 667 patients receiving prophylaxis and dye and in 3 (1.0%) of 301 receiving no prophylaxis and no dye (P = 0.1773). CONCLUSIONS Preoperative prophylaxis was found to reduce the severity, but not the overall incidence, of adverse reactions to isosulfan blue dye. No life-threatening reactions were noted in patients treated with preoperative prophylaxis. Based on these results, the authors now routinely recommend administration of prophylaxis to patients receiving isosulfan blue for lymphatic mapping and sentinel lymph node biopsy. Cancer 2005. © 2005 American Cancer Society.

Study objective To describe the adverse events associated with the intraoperative injection of isosulfan blue in a large group of patients having a wide range of surgical procedures, and to identify risk factors for these events. Design Retrospective chart review. Setting University-affiliated institution specializing in malignancies Patients 1835 patients representing a total of 1852 surgical procedures. Measurements Incidence, type, severity, onset time, duration, management, and the presence of potential risk factors for adverse events. Events were considered "major" if potentially life-threatening hypotension occurred. Main results Adverse events occurred in 28 procedures (1.5%) and 14 of these adverse events (0.75%) were classified as major. The types of events were: skin reactions in 21 patients, hypotension in 14 patients, edema in 1 patients, and unspecified in 1 patient. The time of onset for adverse events was 42.2 ± 53.9 minutes (median, 17.5; range, 1 to 180 min) after isosulfan blue injection, and was significantly longer for minor reactions compared with major events (p = 0.015). The longest adverse event lasted at least 21 hours. Treatment was successful with usual antiallergy/antianaphylaxis medications. Ten patients received diphenhydramine alone, and four patients received intravenous epinephrine infusions. Factors associated with a significantly increased incidence of adverse events were isosulfan blue injection in the vulvar area ( p = 0.000038), and the chronic preoperative use of angiotensin-converting enzyme inhibitors or angiotensin receptor-blocking agents ( p = 0.043). Trends toward an increased risk of an adverse event were noted with isosulfan blue injection in the breast area ( p = 0.19), and having more than one surgical procedure with isosulfan blue ( p = 0.14). Conclusions Although the most frequent adverse event associated with injection of isosulfan blue was a skin reaction, potentially life-threatening hypotension occurred in 0.75% of all procedures. Anesthesiologists must be aware of the variable onset time and potentially prolonged duration of the adverse events. They should recognize the need for extra vigilance in patients with potential risk factors, and have the usual antiallergy/antianaphylaxis medications available for administration if necessary.

We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known asthma loci, established asthma associations at two loci previously implicated in the comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. The enrichment in enhancer marks at asthma risk loci, especially in immune cells, suggested a major role of these loci in the regulation of immunologically related mechanisms.

The underlying ethos of dbGaP is that access to these data by secondary data analysts facilitates advancement of science. NIH has required that genome-wide association study data be deposited in the Database of Genotypes and Phenotypes (dbGaP) since 2003. In 2013, a proposed updated policy extended this requirement to next-generation sequencing data. However, recent literature and anecdotal reports suggest lingering logistical and ethical concerns about subject identifiability, informed consent, publication embargo enforcement, and difficulty in accessing dbGaP data. We surveyed the International Genetic Epidemiology Society (IGES) membership about their experiences. One hundred and seventy five (175) individuals completed the survey, a response rate of 27%. Of respondents who received data from dbGaP (43%), only 32% perceived the application process as easy but most (75%) received data within five months. Remaining challenges include difficulty in identifying an institutional signing official and an overlong application process. Only 24% of respondents had contributed data to dbGaP. Of these, 31% reported local IRB restrictions on data release; an additional 15% had to reconsent study participants before depositing data. The majority of respondents (56%) disagreed that the publication embargo period was sufficient. In response, we recommend longer embargo periods and use of varied data-sharing models rather than a one-size-fits-all approach.

Understanding the mechanisms involved in the development of asthma and allergic diseases is expanding, due in part to sequencing advances that have led to the identification of new viral strains such as human rhinovirus strain C (HRV-C) and the human microbiome project.Recent studies have identified new ways in which viral and microbial exposures in early life interact with host genetic background/variants to modify the risk for developing asthma and allergic diseases. Recent research suggests that HRV-C is the main pathogenic agent associated with infant wheeze, hospitalizations and likely the subsequent development of asthma. Pulmonary He MRI suggests that HRV infection in early childhood and subsequent immune responses initiate airway remodeling. Numerous studies of the microbiome indicate that intestinal and airway microbiome diversity and composition contribute to the cause of asthma and allergic diseases.Susceptibility to asthma and allergic diseases is complex and involves genetic variants and environmental exposures (bacteria, viruses, smoking, and pet ownership), alteration of our microbiome and potentially large-scale manipulation of the environment over the past century.

The brave new world envisioned by proponents of personalized medicine has attracted considerable interest and investment during the past decade or so. The excitement is understandable because personalized medicine promises to drastically improve individual health and make more efficient use of existing resources, changing both health care and public health for the better. Improved use of resources is becoming particularly important, as many national healthcare schemes are straining to maintain affordable health care of acceptable quality under the combined pressures of rising costs, an aging population and the increasing prevalence of many chronic and common diseases. Although not a panacea for all these problems, personalized medicine could theoretically reduce healthcare costs, as an individual’s genetic or other biological information could be used to make better or earlier diagnoses of disease, apply cheaper, preventive measures to decrease disease risk, and make more efficient use of therapeutic options. However, there remains a considerable gap between theory and reality, and we think that the prevailing focus on an individual’s genes and biology insufficiently incorporates the important role of environmental factors in disease etiology and health. Including these factors in our approach to personalized medicine and population health should bring that theory closer to reality. However, it will require a fundamental change to the current research agenda and public health policies to emphasize the role of the social and physical environments and related epigenetic changes.

Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98(th) or

Three multivariate techniques used to derive principal components (PCs) from family data were compared for their ability to model family data and power to detect linkage. Using the simulated data from Genetic Analysis Workshop 12, the five quantitative traits were first adjusted for age, sex, and environmental factors 1 and 2. Then, standard PCs, PCs obtained from between-family covariance, and PCs obtained from within-family genetic covariance were derived and subjected to multivariate sib pair linkage analysis. The standard PCs obtained from the overall correlation matrix allowed identification of key features of the true genetic model more readily than did the other methods. For detection of linkage, standard PCs and PCs obtained from the between-family genetic covariance performed similarly in terms of both power and type 1 error, and both methods performed better than the PCs obtained from within-family genetic covariance.

Summary: Traditional methods of genetic study design and analysis work well under the scenario that a handful of single nucleotide polymorphisms (SNPs) independently contribute to the risk of disease. For complex diseases, susceptibility may be determined not by a single SNP, but rather a complex interplay between SNPs. For large studies involving hundreds of thousands of SNPs, a brute force search of all possible combinations of SNPs associated with disease is not only inefficient, but also results in a multiple testing paradigm, whereby larger and larger sample sizes are needed to maintain statistical power. Pathway-based methods are an example of one of the many approaches in identifying a subset of SNPs to test for interaction. To help determine which SNP–SNP interactions to test, we developed Path, a software application designed to help researchers interface their data with biological information from several bioinformatics resources. To this end, our application brings together currently available information from nine online bioinformatics resources including the National Center for Biotechnology Information (NCBI), Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), UCSC Genome Browser, Seattle SNPs, PharmGKB, Genetic Association Database, the Single Nucleotide Polymorphism database (dbSNP) and the Innate Immune Database (IIDB). Availability: The software, example datasets and tutorials are freely available from http://genapha.icapture.ubc.ca/PathTutorial. Contact: ddaley@mrl.ubc.ca

Study objective To examine current practice regarding the performance of tracheal extubation of adult surgical patients while deeply anesthetized (deep extubation). Design and setting Survey comprised of an anonymous written questionnaire mailed to 1,000 randomly selected active American Society of Anesthesiologists members. Measurements and main results Questionnaires were mailed between February and April 1998. Five hundred eighty-three completed forms were returned, 538 of which were suitable for data analysis. Responses from anesthesiologists who infrequently or never administer general anesthetics to adult surgical patients were excluded. The overall frequency of deep extubation of adults was "never" for 106 respondents (19.7%), "rarely" for 87 (16.2%), and "more frequently" for 345 (64.1%). The most common reasons for never performing deep extubations were lack of necessity and concern regarding potential laryngospasm and aspiration. The most frequent indications for deep extubations were unclipped intracranial aneurysm, reactive airway disease, and open-globe eye surgery. The most frequent contraindications to deep extubations for those who otherwise perform the technique were difficult airway, aspiration risk, and obesity. After performing a deep extubation, 44.0% of respondents remain with the patient in the operating room until he or she is awake. Deep extubations were perceived to have no consistent effect on operating room turnover time by 61.6% of anesthesiologists who perform them. Conclusions Most anesthesiologists in this survey perform deep extubations in adult surgical patients. Lack of necessity and potential respiratory complications were the main reasons cited by those who do not use the technique. Future investigations are necessary to examine the risk-to-benefit ratio of the technique in adults. Our results may be used to determine which potential indications should be examined in such studies and to help delineate the standard of care followed in this country.

Apolipoprotein E (APOE) alleles are associated with longevity in genome-wide scans, with e4 correlated with shorter life, and e2 with longer life, than e3. We hypothesized that rare APOE variants with large individual effects might also contribute to long-term good health. The APOE exons and promoter were resequenced in DNA samples from 376 healthy oldest old aged ≥ 85 yrs with no self-reported history of cancer, cardiovascular disease, diabetes, major pulmonary disease or Alzheimer disease ("Super-Seniors") and 376 population-based controls aged 41-54. Forty variants were observed: 32 were rare (minor allele frequency