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1.  Milwaukee Laboratory System Improvement Program (L-SIP) 
Public Health Reports  2013;128(Suppl 2):40-48.
The Laboratory System Improvement Program (L-SIP) of the Association of Public Health Laboratories aims to improve state public health laboratory (PHL) system performance through continuous quality improvement. We successfully applied this state assessment tool to a local PHL (LPHL) system by tailoring it to reflect local system needs and created an LPHL system definition explaining how a local system differs from, yet complements, a state system.
On November 18, 2010, 75 stakeholders from 40 agencies assessed the Milwaukee, Wisconsin, PHL system, capturing themes, strengths and weaknesses of the system, and scores for each of the 10 Essential Public Health Services. A Laboratory Advisory Committee analyzed assessment results to identify a strategic focus of research and workforce development and define an action plan, which is now being carried out. Milwaukee's L-SIP process is effectively improving LPHL system research and workforce development while raising community awareness of the system.
PMCID: PMC3730004  PMID: 23997302
2.  Adaptability of Contingency Management in Justice Settings: Survey Findings on Attitudes Towards Using Rewards 
Contingency management (CM) is widely recognized as an evidence-based practice, but it is not widely used in either treatment settings or justice settings. CM is perceived as adaptable in justice settings given the natural inclination to use contingencies to improve compliance to desired behaviors. In the Justice Steps implementation study, five federal district court jurisdictions agreed to consider implementing CM in specialized problem-solving courts or probation settings. A baseline survey (n=186) examined the acceptance and feasibility of using rewards as a tool to manage offender compliance. The results of the survey revealed that the majority of respondents believe that rewards are acceptable, with little difference between social and material rewards. Survey findings also showed that female justice workers and those who were not Probation Officers were more accepting of material rewards than their counterparts. Findings are consistent with prior research in drug treatment settings where there is little concern about using rewards.
doi:10.1016/j.jsat.2011.11.004
PMCID: PMC3340513  PMID: 22209658
3.  The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression 
Genetic epidemiology  2011;35(2):93-101.
Although population differences in gene expression have been established, the impact on differential gene expression studies in large populations is not well understood. We describe the effect of self-reported race on a gene expression study of lung function in asthma. We generated gene expression profiles for 254 young adults (205 non-Hispanic whites and 49 African Americans) with asthma on whom concurrent total RNA derived from peripheral blood CD4+ lymphocytes and lung function measurements were obtained. We identified four principal components that explained 62% of the variance in gene expression. The dominant principal component, which explained 29% of the total variance in gene expression, was strongly associated with self-identified race (P<10−16). The impact of these racial differences was observed when we performed differential gene expression analysis of lung function. Using multivariate linear models, we tested whether gene expression was associated with a quantitative measure of lung function: pre-bronchodilator forced expiratory volume in one second (FEV1). Though unadjusted linear models of FEV1 identified several genes strongly correlated with lung function, these correlations were due to racial differences in the distribution of both FEV1 and gene expression, and were no longer statistically significant following adjustment for self-identified race. These results suggest that self-identified race is a critical confounding covariate in epidemiologic studies of gene expression and that, similar to genetic studies, careful consideration of self-identified race in gene expression profiling studies is needed to avoid spurious association.
doi:10.1002/gepi.20560
PMCID: PMC3718033  PMID: 21254216
ancestry; gene expression; population stratification; self-identified race
4.  IL1B Polymorphisms Modulate Cystic Fibrosis Lung Disease 
Pediatric pulmonology  2009;44(6):580-593.
Summary
Rationale: Variability in pulmonary disease severity is found in patients with cystic fibrosis (CF) who have identical mutations in the CF transmembrane conductance regulator (CFTR) gene. We hypothesized that one factor accounting for heterogeneity in pulmonary disease severity is variation in the family of genes affecting the biology of interleukin-1 (IL-1), which impacts acquisition and maintenance of Pseudomonas aeruginosa infection in animal models of chronic infection. Methods: We genotyped 58 single nucleotide polymorphisms (SNPs) in the IL-1 gene cluster in 808 CF subjects from the University of North Carolina and Case Western Reserve University (UNC/CWRU) joint cohort. All were homozygous for ΔF508, and categories of “severe” (cases) or “mild” (control subjects) lung disease were defined by the lowest or highest quartile of forced expired volume (FEV1) for age in the CF population. After adjustment for age and gender, genotypic data were tested for association with lung disease severity. Odds ratios (ORs) comparing severe versus mild CF were also calculated for each genotype (with the homozygote major allele as the reference group) for all 58 SNPs. From these analyses, nine SNPs with a moderate effect size, OR ≤ 0.5or > 1.5, were selected for further testing. To replicate the case-control study results, we genotyped the same nine SNPs in a second population of CF parent-offspring trios (recruited from Children’s Hospital Boston), in which the offspring had similar pulmonary phenotypes. For the trio analysis, both family-based and population-based associations were performed. Results: SNPs rs1143634 and rs1143639 in the IL1B gene demonstrated a consistent association with lung disease severity categories (P < 0.10) and longitudinal analysis of lung disease severity (P < 0.10) in CF in both the case-control and family-based studies. In females, there was a consistent association (false discovery rate adjusted joint P-value < 0.06 for both SNPs) in both the analysis of lung disease severity in the UNC/CWRU cohort and the family-based analysis of affection status. Conclusion: Our findings suggest that IL1β is a clinically relevant modulator of CF lung disease.
doi:10.1002/ppul.21026
PMCID: PMC3716579  PMID: 19431193
gene modifiers; cystic fibrosis; CFTR; IL-1 gene family
5.  Adding positive reinforcement in justice settings: Acceptability and feasibility 
Although contingency management (CM) approaches are among the most promising methods for initiating drug abstinence (S. T. Higgins, S. M. Alessi, & R. L. Dantona, 2002; S. T. Higgins, S. H. Heil, & J. P. Lussier, 2004), adoption and implementation of CM protocols into treatment programs are both challenging and infrequent. In criminal justice agencies, where roughly 70% of clients report substance abuse issues (F. S. Taxman, K. L. Cropsey, D. W. Young, & H. Wexler, 2007), CM interventions are virtually nonexistent. The Justice Steps (JSTEPS) study uses a longitudinal, mixed-method design to examine the implementation of a CM-based protocol in five justice settings. This article presents qualitative data collected during Phase 1 of the JSTEPS project regarding the acceptability and feasibility of CM in these justice settings. The study finds a level of acceptability (find CM tolerable) and feasibility (find CM suitable) within justice agencies, but with some challenges. These challenges are reflected in the following: (a) incorporating too many desired target behaviors into CM models; (b) facing intraorganizational challenges when designing CM systems; and (c) emphasizing sanctions over rewards despite the evidence-base for positive reinforcers. These findings have implications for advancing the dissemination, adoption, and implementation of evidence-based treatments (and CM in particular) in criminal justice settings.
doi:10.1016/j.jsat.2011.08.002
PMCID: PMC3674847  PMID: 21940135
Contingency management; Drug abstinence and treatment; Rewards/incentives; Criminal justice; Acceptability and feasibility
6.  Genomewide Association between GLCCI1 and Response to Glucocorticoid Therapy in Asthma 
The New England journal of medicine  2011;365(13):1173-1183.
BACKGROUND
The response to treatment for asthma is characterized by wide interindividual variability, with a significant number of patients who have no response. We hypothesized that a genomewide association study would reveal novel pharmacogenetic determinants of the response to inhaled glucocorticoids.
METHODS
We analyzed a small number of statistically powerful variants selected on the basis of a family-based screening algorithm from among 534,290 single-nucleotide polymorphisms (SNPs) to determine changes in lung function in response to inhaled glucocorticoids. A significant, replicated association was found, and we characterized its functional effects.
RESULTS
We identified a significant pharmacogenetic association at SNP rs37972, replicated in four independent populations totaling 935 persons (P = 0.0007), which maps to the glucocorticoid-induced transcript 1 gene (GLCCI1) and is in complete linkage disequilibrium (i.e., perfectly correlated) with rs37973. Both rs37972 and rs37973 are associated with decrements in GLCCI1 expression. In isolated cell systems, the rs37973 variant is associated with significantly decreased luciferase reporter activity. Pooled data from treatment trials indicate reduced lung function in response to inhaled glucocorticoids in subjects with the variant allele (P = 0.0007 for pooled data). Overall, the mean (± SE) increase in forced expiratory volume in 1 second in the treated subjects who were homozygous for the mutant rs37973 allele was only about one third of that seen in similarly treated subjects who were homozygous for the wild-type allele (3.2 ± 1.6% vs. 9.4 ± 1.1%), and their risk of a poor response was significantly higher (odds ratio, 2.36; 95% confidence interval, 1.27 to 4.41), with genotype accounting for about 6.6% of overall inhaled glucocorticoid response variability.
CONCLUSIONS
A functional GLCCI1 variant is associated with substantial decrements in the response to inhaled glucocorticoids in patients with asthma. (Funded by the National Institutes of Health and others; ClinicalTrials.gov number, NCT00000575.)
doi:10.1056/NEJMoa0911353
PMCID: PMC3667396  PMID: 21991891
7.  On the genome-wide analysis of copy number variants in family-based designs: Methods for combining family-based and population based information for testing dichotomous or quantitative traits, or completely ascertained samples 
Genetic Epidemiology  2010;34(6):582-590.
We propose a new approach for the analysis of copy number variants (CNVs)for genome-wide association studies in family-based designs. Our new overall association test combines the between-family component and the within-family component of the data so that the new test statistic is fully efficient and, at the same time, achieves the complete robustness against population-admixture and stratification, as classical family-based association tests that are based only on the between-family component. Although all data are incorporated into the test statistic, an adjustment for genetic confounding is not needed, not even for the between-family component. The new test statistic is valid for testing either quantitative or dichotomous phenotypes. If external CNV data are available, the approach can also be used in completely ascertained samples. Similar to the approach by Ionita-Laza et al.(1), the proposed test statistic does not required a CNV-calling algorithm and is based directly on the CNV probe intensity data. We show, via simulation studies, that our methodology increases the power of the FBAT statistic to levels comparable to those of population-based designs. The advantages of the approach in practice are demonstrated by an application to a genome-wide association study for body mass index (BMI).
doi:10.1002/gepi.20515
PMCID: PMC3349936  PMID: 20718041
8.  Nurse Case Management and Housing Interventions Reduce Allergen Exposures: The Milwaukee Randomized Controlled Trial 
Public Health Reports  2011;126(Suppl 1):89-99.
Objective
We examined the impact of a combination of home environmental interventions and nurse case management services on total settled dust loadings and on allergen concentrations in the homes of asthmatic children.
Methods
Using a randomized longitudinal controlled trial study design, we randomly assigned homes of asthmatic children in Milwaukee to either a control (n=64) or an intervention (n=57) group. Control group homes received a visual assessment, education, bed/pillow dust mite encasings, and treatment of lead-based paint hazards. The intervention group received these same services plus nurse case management that included tailored, individual asthma action plans, provision of minor home repairs, home cleaning using special vacuuming and wet washing, and integrated pest management. Dust vacuum samples were collected from measured surface areas of floors in the TV room, kitchen, and child's bedroom at baseline and at three-, six-, and 12-month follow-up visits. Dust loading (mass per surface area) is a means of measuring total dust and the total amount of allergen present.
Results
For the intervention group, geometric mean dust loadings declined significantly from baseline (39 milligrams per square foot [mg/ft2]) to post-intervention (11 mg/ft2) (p<0.001). Baseline dust loading, treatment group, visit, and season were significant predictors of follow-up dust loadings. Mean post-intervention dust loadings were 72% higher in the control group. The total amount of allergen in settled house dust declined significantly following the intervention because total dust loading declined; the concentration of allergens in settled dust did not change significantly.
Conclusion
The combination of nurse case management and home environmental interventions promotes collaboration between health and housing professionals and is effective in reducing exposures to allergens in settled dust.
PMCID: PMC3072907  PMID: 21563716
9.  Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes 
Human Molecular Genetics  2010;19(23):4745-4757.
Genome-wide association studies of human gene expression promise to identify functional regulatory genetic variation that contributes to phenotypic diversity. However, it is unclear how useful this approach will be for the identification of disease-susceptibility variants. We generated gene expression profiles for 22 184 mRNA transcripts using RNA derived from peripheral blood CD4+ lymphocytes, and genome-wide genotype data for 516 512 autosomal markers in 200 subjects. We screened for cis-acting variants by testing variants mapping within 50 kb of expressed transcripts for association with transcript abundance using generalized linear models. Significant associations were identified for 1585 genes at a false discovery rate of 0.05 (corresponding to P-values ranging from 1 × 10−91 to 7 × 10−4). Importantly, we identified evidence of regulatory variation for 119 previously mapped disease genes, including 24 examples where the variant with the strongest evidence of disease-association demonstrates strong association with specific transcript abundance. The prevalence of cis-acting variants among disease-associated genes was 63% higher than the genome-wide rate in our data set (P = 6.41 × 10−6), and although many of the implicated loci were associated with immune-related diseases (including asthma, connective tissue disorders and inflammatory bowel disease), associations with genes implicated in non-immune-related diseases including lipid profiles, anthropomorphic measurements, cancer and neurologic disease were also observed. Genetic variants that confer inter-individual differences in gene expression represent an important subset of variants that contribute to disease susceptibility. Population-based integrative genetic approaches can help identify such variation and enhance our understanding of the genetic basis of complex traits.
doi:10.1093/hmg/ddq392
PMCID: PMC2972694  PMID: 20833654
10.  An omnibus test for family-based association studies with multiple SNPs and multiple phenotypes 
We propose an omnibus family-based association test (MFBAT) that can be applied to multiple markers and multiple phenotypes and that has only one degree of freedom. The proposed test statistic extends current FBAT methodology to incorporate multiple markers as well as multiple phenotypes. Using simulation studies, power estimates for the proposed methodology are compared with the standard methodologies. On the basis of these simulations, we find that MFBAT substantially outperforms other methods, including haplotypic approaches and doing multiple tests with single single-nucleotide polymorphisms (SNPs) and single phenotypes. The practical relevance of the approach is illustrated by an application to asthma in which SNP/phenotype combinations are identified and reach overall significance that would not have been identified using other approaches. This methodology is directly applicable to cases in which there are multiple SNPs, such as candidate gene studies, cases in which there are multiple phenotypes, such as expression data, and cases in which there are multiple phenotypes and genotypes, such as genome-wide association studies that incorporate expression profiles as phenotypes. This program is available in the PBAT analysis package.
doi:10.1038/ejhg.2009.221
PMCID: PMC2874662  PMID: 20087406
family-based association testing (FBAT); genome-wide association studies; FBAT-PC; multiple marker; multiple phenotypes; multiple testing
11.  Estradiol suppresses NF-κB activation through coordinated regulation of let-7a and miR-125b in primary human macrophages 
Previous findings suggest that estradiol has a suppressive effect on TNF-α, but the mechanism by which estradiol regulates TNF-α expression in primary human macrophages is unknown. Herein, we demonstrate that pretreatment of human macrophages with estradiol attenuates LPS-induced TNF-α expression through suppression of NF-κB activation. Furthermore, we show that activation of macrophages with LPS decreases expression of κB-Ras2, an inhibitor of NF-κB signaling. Estradiol pre-treatment abrogates this decrease, leading to enhanced expression of κB-Ras2 with LPS stimulation. Additionally, we have identified two miRNAs, let-7a and miR-125b, that target the κB-Ras2 3′UTR. LPS induces let-7a and inhibits miR-125b expression in human macrophages and pre-treatment with estradiol abrogates these effects. 3′UTR reporter assays demonstrate that let-7a destabilizes the κB-Ras2 3′UTR while miR-125b enhances its stability, resulting in decreased κB-Ras2 in response to LPS. Our data suggest that pre-treatment with estradiol reverses this effect. We propose a novel mechanism for estradiol inhibition of LPS-induced NF-κB signaling in which κB-Ras2 expression is induced by estradiol via regulation of let-7a and miR-125b. These findings are significant in that they are the first to demonstrate that estradiol represses NF-κB activation through induction of κB-Ras2, a key inhibitor of NF-κB signaling.
This is an author-produced version of a manuscript accepted for publication in The Journal of Immunology (The JI). The American Association of Immunologists, Inc. (AAI), publisher of The JI, holds the copyright to this manuscript. This version of the manuscript has not yet been copyedited or subjected to editorial proofreading by The JI; hence, it may differ from the final version published in The JI (online and in print). AAI (The JI) is not liable for errors or omissions in this author-produced version of the manuscript or in any version derived from it by the U.S. National Institutes of Health or any other third party. The final, citable version of record can be found at www.jimmunol.org.
doi:10.4049/jimmunol.0903463
PMCID: PMC2882792  PMID: 20351193
12.  The CD4+ T-cell transcriptome and serum IgE in asthma: IL17RB and the role of sex 
Background
The relationships between total serum IgE levels and gene expression patterns in peripheral blood CD4+ T cells (in all subjects and within each sex specifically) are not known.
Methods
Peripheral blood CD4+ T cells from 223 participants from the Childhood Asthma Management Program (CAMP) with simultaneous measurement of IgE. Total RNA was isolated, and expression profiles were generated with Illumina HumanRef8 v2 BeadChip arrays. Modeling of the relationship between genome-wide gene transcript levels and IgE levels was performed in all subjects, and stratified by sex.
Results
Among all subjects, significant evidence for association between gene transcript abundance and IgE was identified for a single gene, the interleukin 17 receptor B (IL17RB), explaining 12% of the variance (r2) in IgE measurement (p value = 7 × 10-7, 9 × 10-3 after adjustment for multiple testing). Sex stratified analyses revealed that the correlation between IL17RB and IgE was restricted to males only (r2 = 0.19, p value = 8 × 10-8; test for sex-interaction p < 0.05). Significant correlation between gene transcript abundance and IgE level was not found in females. Additionally we demonstrated substantial sex-specific differences in IgE when considering multi-gene models, and in canonical pathway analyses of IgE level.
Conclusions
Our results indicate that IL17RB may be the only gene expressed in CD4+ T cells whose transcript measurement is correlated with the variation in IgE level in asthmatics. These results provide further evidence sex may play a role in the genomic regulation of IgE.
doi:10.1186/1471-2466-11-17
PMCID: PMC3080837  PMID: 21473777
13.  A Role for Wnt Signaling Genes in the Pathogenesis of Impaired Lung Function in Asthma 
Rationale: Animal models demonstrate that aberrant gene expression in utero can result in abnormal pulmonary phenotypes.
Objectives: We sought to identify genes that are differentially expressed during in utero airway development and test the hypothesis that variants in these genes influence lung function in patients with asthma.
Methods: Stage 1 (Gene Expression): Differential gene expression analysis across the pseudoglandular (n = 27) and canalicular (n = 9) stages of human lung development was performed using regularized t tests with multiple comparison adjustments. Stage 2 (Genetic Association): Genetic association analyses of lung function (FEV1, FVC, and FEV1/FVC) for variants in five differentially expressed genes were conducted in 403 parent-child trios from the Childhood Asthma Management Program (CAMP). Associations were replicated in 583 parent-child trios from the Genetics of Asthma in Costa Rica study.
Measurements and Main Results: Of the 1,776 differentially expressed genes between the pseudoglandular (gestational age: 7–16 wk) and the canalicular (gestational age: 17–26 wk) stages, we selected 5 genes in the Wnt pathway for association testing. Thirteen single nucleotide polymorphisms in three genes demonstrated association with lung function in CAMP (P < 0.05), and associations for two of these genes were replicated in the Costa Ricans: Wnt1-inducible signaling pathway protein 1 with FEV1 (combined P = 0.0005) and FVC (combined P = 0.0004), and Wnt inhibitory factor 1 with FVC (combined P = 0.003) and FEV1/FVC (combined P = 0.003).
Conclusions: Wnt signaling genes are associated with impaired lung function in two childhood asthma cohorts. Furthermore, gene expression profiling of human fetal lung development can be used to identify genes implicated in the pathogenesis of lung function impairment in individuals with asthma.
doi:10.1164/rccm.200907-1009OC
PMCID: PMC2822972  PMID: 19926868
asthma; lung development; lung function; genetic variation; gene expression
14.  An omnibus test for family-based association studies with multiple SNPs and multiple phenotypes 
We propose an omnibus family-based association test (MFBAT), that can be applied to multiple markers and multiple phenotypes and that has only 1 degree of freedom. The proposed test statistic extends current FBAT methodology to incorporate multiple markers as well as multiple phenotypes. Using simulation studies, power estimates for the proposed methodology are compared with the standard methodologies. Based on these simulations, we find that MFBAT substantially outperforms other methods including some haplotypic approaches and doing multiple tests with single SNPs and single phenotypes. The practical relevance of the approach is illustrated by an application to asthma where SNPs/phenotype combinations are identified and reach overall significance that would not have been identified using other approaches. This methodology is directly applicable to cases where there are multiple SNPs, such as candidate gene studies, cases where there are multiple phenotypes, such as expression data, and cases where there are multiple phenotypes and genotypes, such as genome-wide association studies that incorporate expression profiles as phenotypes. This program is available in the PBAT analysis package1.
doi:10.1038/ejhg.2009.221
PMCID: PMC2874662  PMID: 20087406
Family-based association testing (FBAT); genome-wide association studies; FBAT-PC; multiple marker; multiple phenotypes; multiple testing
15.  The interaction of GSTM1 null variants with tobacco smoke exposure and the development of childhood asthma 
Background
The glutathione S-transferase M1 (GSTM1) null variant is a common copy number variant associated with adverse pulmonary outcomes, including asthma and airflow obstruction, with evidence of important gene-by-environment interactions with exposures to oxidative stress.
Objective
To explore the joint interactive effects of GSTM1 copy number and tobacco smoke exposure on the development of asthma and asthma-related phenotypes in a family-based cohort of childhood asthmatics.
Methods
We performed quantitative PCR-based genotyping for GSTM1 copy number in children of self-reported white ancestry with mild to moderate asthma in the Childhood Asthma Management Program. Questionnaire data regarding intrauterine (IUS) and postnatal, longitudinal environmental tobacco smoke exposure were available. We performed both family-based and population-based tests of association for the interaction between GSTM1 copy number and tobacco smoke exposure with asthma and asthma-related phenotypes.
Results
Associations of GSTM1 null variants with asthma (p= .03), younger age of asthma symptom onset (p=.03), and greater airflow obstruction (reduced FEV1/FVC, p=.01) were observed among the 50 children (10% of the cohort) with exposure to IUS. In contrast, no associations were observed between GSTM1 null variants and asthma-related phenotypes among children without IUS exposure. Presence of at least one copy of GSTM1 conferred protection.
Conclusion
These findings support an important gene-by-environment interaction between two common factors: increased risk of asthma and asthma-related phenotypes conferred by GSTM1-null homozygosity in children is restricted to those with a history of IUS exposure.
doi:10.1111/j.1365-2222.2009.03372.x
PMCID: PMC2773694  PMID: 19860819
Asthma; GSTM1; copy number variation (CNV); gene by environment; intrauterine smoke exposure; tobacco smoke
16.  Clinical Predictors and Outcomes of Consistent Bronchodilator Response in the Childhood Asthma Management Program 
Background
Among asthmatics, bronchodilator response (BDR) to inhaled ß2- adrenergic agonists is variable, and the significance of a consistent response over time is unknown.
Objective
We assessed baseline clinical variables and determined the clinical outcomes associated with a consistently positive BDR over 4 years in children with mild-moderate persistent asthma.
Methods
In the 1,041 participants in the Childhood Asthma Management Program (CAMP), subjects with a change in FEV1 of 12% or greater (and 200mLs) after inhaled ß2 agonist at each of their yearly follow-up visits (consistent BDR) were compared with those who did not have a consistent BDR.
Results
We identified 52 children with consistent BDR over the 4-year trial. Multivariable logistic regression modeling demonstrated that baseline pre-bronchodilator FEV1 (OR=0.71, p<0.0001), log 10 IgE level (OR=1.97, p=0.002), and lack of treatment with inhaled corticosteroids (OR=0.31, p=0.009) were associated with a consistent BDR. Individuals who had a consistent BDR had more hospital visits (p=0.007), required more prednisone bursts (p=0.0007), had increased nocturnal awakenings due to asthma (p<0.0001), and missed more days of school (p=0.03) than non-responders during the 4-year follow-up.
Conclusions
We have identified predictors of consistent BDR and determined that this phenotype is associated with poor clinical outcomes.
doi:10.1016/j.jaci.2008.09.004
PMCID: PMC2947830  PMID: 18848350
asthma; consistent bronchodilator response; outcomes
17.  Asthma-susceptibility variants identified using probands in case-control and family-based analyses 
BMC Medical Genetics  2010;11:122.
Background
Asthma is a chronic respiratory disease whose genetic basis has been explored for over two decades, most recently via genome-wide association studies. We sought to find asthma-susceptibility variants by using probands from a single population in both family-based and case-control association designs.
Methods
We used probands from the Childhood Asthma Management Program (CAMP) in two primary genome-wide association study designs: (1) probands were combined with publicly available population controls in a case-control design, and (2) probands and their parents were used in a family-based design. We followed a two-stage replication process utilizing three independent populations to validate our primary findings.
Results
We found that single nucleotide polymorphisms with similar case-control and family-based association results were more likely to replicate in the independent populations, than those with the smallest p-values in either the case-control or family-based design alone. The single nucleotide polymorphism that showed the strongest evidence for association to asthma was rs17572584, which replicated in 2/3 independent populations with an overall p-value among replication populations of 3.5E-05. This variant is near a gene that encodes an enzyme that has been implicated to act coordinately with modulators of Th2 cell differentiation and is expressed in human lung.
Conclusions
Our results suggest that using probands from family-based studies in case-control designs, and combining results of both family-based and case-control approaches, may be a way to augment our ability to find SNPs associated with asthma and other complex diseases.
doi:10.1186/1471-2350-11-122
PMCID: PMC2927535  PMID: 20698975
18.  Assessing the Reproducibility of Asthma Candidate Gene Associations, Using Genome-wide Data 
Rationale: Association studies have implicated many genes in asthma pathogenesis, with replicated associations between single-nucleotide polymorphisms (SNPs) and asthma reported for more than 30 genes. Genome-wide genotyping enables simultaneous evaluation of most of this variation, and facilitates more comprehensive analysis of other common genetic variation around these candidate genes for association with asthma.
Objectives: To use available genome-wide genotypic data to assess the reproducibility of previously reported associations with asthma and to evaluate the contribution of additional common genetic variation surrounding these loci to asthma susceptibility.
Methods: Illumina Human Hap 550Kv3 BeadChip (Illumina, San Diego, CA) SNP arrays were genotyped in 422 nuclear families participating in the Childhood Asthma Management Program. Genes with at least one SNP demonstrating prior association with asthma in two or more populations were tested for evidence of association with asthma, using family-based association testing.
Measurements and Main Results: We identified 39 candidate genes from the literature, using prespecified criteria. Of the 160 SNPs previously genotyped in these 39 genes, 10 SNPs in 6 genes were significantly associated with asthma (including the first independent replication for asthma-associated integrin β3 [ITGB3]). Evaluation of 619 additional common variants included in the Illumina 550K array revealed additional evidence of asthma association for 15 genes, although none were significant after adjustment for multiple comparisons.
Conclusions: We replicated asthma associations for a minority of candidate genes. Pooling genome-wide association study results from multiple studies will increase the power to appreciate marginal effects of genes and further clarify which candidates are true “asthma genes.”
doi:10.1164/rccm.200812-1860OC
PMCID: PMC2695495  PMID: 19264973
asthma; replication; single-nucleotide polymorphism; integrin β3; association
19.  Functional Expression of Pattern Recognition Receptors in Tissues of the Human Female Reproductive Tract 
The human female reproductive tract (FRT) must balance the requirements of procreation with the demands of protection from pathogen invasion. We hypothesize that the FRT expresses functional pattern recognition receptors (PRRs), including Toll-like Receptors (TLRs) and nucleotide-binding oligomerization domain (NOD) proteins that may mediate these tasks. Expression of PRRs was evaluated in FRT tissues by RT-PCR. PRR function within FRT tissue cells was determined by CXCL8 (IL-8) production in response to treatment with PRR agonists. We now report that TLRs 7–9 are expressed in Fallopian tube, uterine endometrium, cervix and ectocervix, while TLR10 expression is restricted to Fallopian tube. NOD1 and NOD2 and the signal transducer RICK were detected in all FRT tissues. Stimulation of FRT tissue cells with PRR ligands resulted in secretion of CXCL8. Results of these studies indicate that PRR are functionally expressed in FRT tissues, and suggest that these receptors mediate microbial recognition and immune defense in the reproductive tract.
doi:10.1016/j.jri.2008.12.004
PMCID: PMC2744441  PMID: 19406482
Human; Female; Reproductive; TLR; NOD
20.  Variants in TGFB1, Dust Mite Exposure, and Disease Severity in Children with Asthma 
Rationale: Polymorphisms in the gene for transforming growth factor-β1 (TGFB1) have been associated with asthma, but not with airway responsiveness or disease exacerbations in subjects with asthma.
Objectives: To test for association between single nucleotide polymorphisms (SNPs) in TGFB1 and markers of asthma severity in childhood.
Methods: We tested for the association between nine SNPs in TGFB1 and indicators of asthma severity (lung function, airway responsiveness, and disease exacerbations) in two cohorts: 416 Costa Rican parent-child trios and 465 families of non-Hispanic white children in the Childhood Asthma Management Program (CAMP). We also tested for the interaction between these polymorphisms and exposure to dust mite allergen on asthma severity.
Measurements and Main Results: The A allele of promoter SNP rs2241712 was associated with increased airway responsiveness in Costa Rica (P = 0.0006) and CAMP (P = 0.005), and the C allele of an SNP in the promoter region (rs1800469) was associated with increased airway responsiveness in both cohorts (P ≤ 0.01). Dust mite exposure modified the effect of the C allele of exonic SNP rs1800471 on airway responsiveness (P = 0.03 for interactions in both cohorts). The T allele of a coding SNP (rs1982073) was associated with a reduced risk of asthma exacerbations in Costa Rica (P = 0.009) and CAMP (P = 0.005). Dust mite exposure also significantly modified the effect of the A allele of the promoter SNP rs2241712 on asthma exacerbations in both cohorts.
Conclusions: SNPs in TGFB1 are associated with airway responsiveness and disease exacerbations in children with asthma. Moreover, dust mite exposure may modify the effect of TGFB1 SNPs on airway responsiveness and asthma exacerbations.
doi:10.1164/rccm.200808-1268OC
PMCID: PMC2648908  PMID: 19096005
airway responsiveness; asthma; dust mite allergen; single nucleotide polymorphisms; transforming growth factor-β1
21.  Estradiol Regulates Expression of Estrogen Receptor ERα46 in Human Macrophages 
PLoS ONE  2009;4(5):e5539.
Background
Monocytes and macrophages are key innate immune effector cells that produce cytokines and chemokines upon activation. We and others have shown that 17β-estradiol (E2) has a direct role in the modulation of monocyte and macrophage immune function. However, relatively little is known about the ability of E2 to regulate isoform expression of estrogen receptors (ERs) in these cells.
Methodology/Principal Findings
In this study, we quantify expression of ERα and ERβ in human monocytes and macrophages. We also show for the first time that the N-terminal truncated ERα variant, ERα46, is expressed in both cell types. Promoter utilization studies reveal that transcription of ERα in both cell types occurs from upstream promoters E and F. Treatment with E2 induces ERα expression in macrophages but has no effect on ERβ levels in either cell type. During monocyte-to-macrophage differentiation, ERα is upregulated in a time-dependent manner. Previous studies by our group demonstrated that E2 treatment attenuates production of the chemokine CXCL8 in an ER-dependent manner. We now show that ERα expression levels parallel the ability of E2 to suppress CXCL8 production.
Conclusions/Significance
This work demonstrates for the first time that human macrophages predominantly express the truncated ER variant ERαp46, which is estradiol-inducible. This is mediated through usage of the ERα F promoter. Alternative promoter usage may account for tissue and cell type-specific differences in estradiol-induced effects on gene expression. These studies signify the importance of ERα expression and regulation in the ability of E2 to modulate innate immune responses.
doi:10.1371/journal.pone.0005539
PMCID: PMC2678254  PMID: 19440537
22.  Comprehensive Testing of Positionally Cloned Asthma Genes in Two Populations 
Rationale: Replication of gene-disease associations has become a requirement in complex trait genetics.
Objectives: In studies of childhood asthma from two different ethnic groups, we attempted to replicate associations with five potential asthma susceptibility genes previously identified by positional cloning.
Methods: We analyzed two family-based samples ascertained through an asthmatic proband: 497 European-American children from the Childhood Asthma Management Program and 439 Hispanic children from the Central Valley of Costa Rica. We genotyped 98 linkage disequilibrium–tagging single-nucleotide polymorphisms (SNPs) in five genes: ADAM33, DPP10, GPR154 (HUGO name: NPSR1), HLA-G, and the PHF11 locus (includes genes SETDB2 and RCBTB1). SNPs were tested for association with asthma and two intermediate phenotypes: airway hyperresponsiveness and total serum immunoglobulin E levels.
Measurements and Main Results: Despite differing ancestries, linkage disequilibrium patterns were similar in both cohorts. Of the five evaluated genes, SNP-level replication was found only for GPR154 (NPSR1). In this gene, three SNPs were associated with asthma in both cohorts, although the opposite alleles were associated in either study. Weak evidence for locus-level replication with asthma was found in the PHF11 locus, although there was no overlap in the associated SNP across the two cohorts. No consistent associations were observed for the three other genes.
Conclusions: These results provide some further support for the role of genetic variation in GPR154 (NPSR1) and PHF11 in asthma susceptibility and also highlight the challenges of replicating genetic associations in complex traits such as asthma, even for genes identified by linkage analysis.
doi:10.1164/rccm.200704-592OC
PMCID: PMC2048676  PMID: 17702965
bronchial hyperreactivity; immunoglobulin E; linkage disequilibrium; NPSR1; single-nucleotide polymorphism
23.  Screening and Replication using the Same Data Set: Testing Strategies for Family-Based Studies in which All Probands Are Affected 
PLoS Genetics  2008;4(9):e1000197.
For genome-wide association studies in family-based designs, we propose a powerful two-stage testing strategy that can be applied in situations in which parent-offspring trio data are available and all offspring are affected with the trait or disease under study. In the first step of the testing strategy, we construct estimators of genetic effect size in the completely ascertained sample of affected offspring and their parents that are statistically independent of the family-based association/transmission disequilibrium tests (FBATs/TDTs) that are calculated in the second step of the testing strategy. For each marker, the genetic effect is estimated (without requiring an estimate of the SNP allele frequency) and the conditional power of the corresponding FBAT/TDT is computed. Based on the power estimates, a weighted Bonferroni procedure assigns an individually adjusted significance level to each SNP. In the second stage, the SNPs are tested with the FBAT/TDT statistic at the individually adjusted significance levels. Using simulation studies for scenarios with up to 1,000,000 SNPs, varying allele frequencies and genetic effect sizes, the power of the strategy is compared with standard methodology (e.g., FBATs/TDTs with Bonferroni correction). In all considered situations, the proposed testing strategy demonstrates substantial power increases over the standard approach, even when the true genetic model is unknown and must be selected based on the conditional power estimates. The practical relevance of our methodology is illustrated by an application to a genome-wide association study for childhood asthma, in which we detect two markers meeting genome-wide significance that would not have been detected using standard methodology.
Author Summary
The current state of genotyping technology has enabled researchers to conduct genome-wide association studies of up to 1,000,000 SNPs, allowing for systematic scanning of the genome for variants that might influence the development and progression of complex diseases. One of the largest obstacles to the successful detection of such variants is the multiple comparisons/testing problem in the genetic association analysis. For family-based designs in which all offspring are affected with the disease/trait under study, we developed a methodology that addresses this problem by partitioning the family-based data into two statistically independent components. The first component is used to screen the data and determine the most promising SNPs. The second component is used to test the SNPs for association, where information from the screening is used to weight the SNPs during testing. This methodology is more powerful than standard procedures for multiple comparisons adjustment (i.e., Bonferroni correction). Additionally, as only one data set is required for screening and testing, our testing strategy is less susceptible to study heterogeneity. Finally, as many family-based studies collect data only from affected offspring, this method addresses a major limitation of previous methodologies for multiple comparisons in family-based designs, which require variation in the disease/trait among offspring.
doi:10.1371/journal.pgen.1000197
PMCID: PMC2529406  PMID: 18802462
24.  Polymorphisms in IL12A and cockroach allergy in children with asthma 
Background
IL12A has been implicated in T-cell development and may thus influence the development of atopy and allergic diseases.
Methods
We tested for association between four linkage disequilibrium (LD)-tagging SNPs (rs2243123, rs2243151, rs668998, and rs17826053) in IL12A and asthma and allergy-related (serum total and allergen-specific IgE, and skin test reactivity [STR] to two common allergens) phenotypes in two samples: 417 Costa Rican children with asthma and their parents, and 470 families of 503 white children in the Childhood Asthma Management Program (CAMP). The analysis was conducted using the family-based association test (FBAT) statistic implemented in the PBAT program.
Results
Among Costa Rican children with asthma, homozygosity for the minor allele of each of two SNPs in IL12A (rs2243123 and rs2243151) was associated with increased risks of STR to American cockroach (P ≤ 0.03 for both SNPs), STR to German cockroach (P ≤ 0.01 for both SNPs), and having a positive IgE to German cockroach (P < 0.05 for both SNPs). Among children in CAMP, homozygosity for the minor allele of SNP rs2243151 in IL12A was inversely associated with STR to German cockroach (P = 0.03) and homozygosity for the minor allele of SNP rs17826053 in IL12A was associated with increased risks of STR to American cockroach (P = 0.01) and STR to German cockroach (P = 0.007). There was no significant association between any SNP in IL12A and asthma, STR to dust mite, or total IgE in Costa Rica or CAMP.
Conclusion
Our findings suggest that variants in IL12A influence cockroach allergy among children with asthma.
doi:10.1186/1476-7961-6-6
PMCID: PMC2525650  PMID: 18671862
25.  Genomic screening in family-based association testing 
BMC Genetics  2005;6(Suppl 1):S115.
Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of disease susceptibility loci, and identify new genetic determinants of disease. However, the problem of multiple comparisons threatens to diminish any potential gains from this newly available data. To circumvent the multiple comparisons issue, we utilize a recently developed screening technique using family-based association testing. This screening methodology allows for the identification of the most promising single-nucleotide polymorphisms for testing without biasing the nominal significance level of our test statistic. We compare the results of our screening technique across univariate and multivariate family-based association tests. From our analyses, we observe that the screening technique, applied to different settings, is fairly consistent in identifying optimal markers for testing. One of the identified markers, TSC0047225, was significantly associated with both the ttth1 (p = 0.004) and ttth1-ttth4 (p = 0.004) phenotype(s). We find that both univariate- and multivariate-based screening techniques are powerful tools for detecting an association.
doi:10.1186/1471-2156-6-S1-S115
PMCID: PMC1866823  PMID: 16451572

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