Genetic ancestry in lung-function predictions

Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations

Accumulated evidence supports the contribution of genetic factors in modulating airway function, especially ancestry. We investigated whether genetic polymorphisms can affect lung function in a mixed Brazilian child population using the admixture mapping strategy through RFMix software version 1.5.4 (Stanford University, Stanford, CA, USA), followed by fine mapping, to identify regions whereby local African or European ancestry is associated with lung function measured by the forced expiratory volume in the first second (FEV1)/forced vital capacity (FVC) ratio, an indicator of airway obstruction. The research cohort included 958 individuals aged 4 to 11 years enrolled in the SCAALA (Social Change, Asthma, Allergy in Latin America) Program. We identified that African ancestry at 17q21.31, 10q22.2, and 2p23.1 regions was associated with lower lung function measured by FEV1/FVC p < 1.9 × 10-4. In contrast, European ancestry at 17q21.31 showed an opposite effect. Fine mapping pointed out 5 single nucleotide polymorphisms (SNPs) also associated in our replication cohort (rs10999948, rs373831475, rs8068257, rs6744555, and rs1520322). Our results suggest that genomic regions associated with ancestry may contribute to differences in lung function measurements in African American children in Brazil replicated in a cohort of Brazilian adults. The analysis strategy used in this work is especially important for phenotypes, such as lung function, which has considerable disparities in terms of measurements across different populations.

On the cross-population generalizability of gene expression prediction models

The genetic control of gene expression is a core component of human physiology. For the past several years, transcriptome-wide association studies have leveraged large datasets of linked genotype and RNA sequencing information to create a powerful gene-based test of association that has been used in dozens of studies. While numerous discoveries have been made, the populations in the training data are overwhelmingly of European descent, and little is known about the generalizability of these models to other populations. Here, we test for cross-population generalizability of gene expression prediction models using a dataset of African American individuals with RNA-Seq data in whole blood. We find that the default models trained in large datasets such as GTEx and DGN fare poorly in African Americans, with a notable reduction in prediction accuracy when compared to European Americans. We replicate these limitations in cross-population generalizability using the five populations in the GEUVADIS dataset. Via realistic simulations of both populations and gene expression, we show that accurate cross-population generalizability of transcriptome prediction only arises when eQTL architecture is substantially shared across populations. In contrast, models with non-identical eQTLs showed patterns similar to real-world data. Therefore, generating RNA-Seq data in diverse populations is a critical step towards multi-ethnic utility of gene expression prediction.

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures

Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.

Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction

Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV1), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV1 on chromosome 12 in 867 African American children with asthma (P = 1.26 × 10-8, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV1 Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure (P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV1, possibly mediated through KITLG, in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG, which has established a role in orchestrating allergic inflammation in asthma.

Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans

Admixture mapping has led to the discovery of many genes associated with differential disease risk by ancestry, highlighting the importance of ancestry-based approaches to association studies. However, the potential of admixture mapping in deciphering the interplay between genes and environment exposures has been seldom explored. Here we performed a genome-wide screening of local ancestry-smoking interactions for five spirometric lung function phenotypes in 3300 African Americans from the COPDGene study. To account for population structure and outcome heterogeneity across exposure groups, we developed a multi-component linear mixed model for mapping gene-environment interactions and empirically showed its robustness and increased power. When applied to the COPDGene study, our approach identified two 11p15.2-3 and 2q37 loci, exhibiting local ancestry-smoking interactions at genome-wide significant level, which would have been missed by standard single-nucleotide polymorphism analyses. These two loci harbor the PARVA and RAB17 genes previously recognized to be involved in smoking behavior. Overall, our study provides the first evidence for potential synergistic effects between African ancestry and smoking on pulmonary function, and underlines the importance of ethnic diversity in genetic studies.

Association of birthplace and occupational exposures with chronic bronchitis in US Hispanics/Latinos, 2008-2011

OBJECTIVES

In the US, chronic bronchitis (CB) is common and is associated with substantial morbidity and mortality. Data on CB in the Hispanic/Latino population-a large, diverse US minority-are scarce. We aimed to test whether the prevalence of CB varies across Hispanic/Latino heritages and to identify CB risk factors, including occupational exposures, in this population.

METHODS

We analysed data from the Hispanic Community Health Study/Study of Latinos, a US population-based probability sample of participants aged 18-74 years (n=16 415) including those with Mexican, Puerto Rican, Dominican, Cuban, Central American and South American heritages. Participants who had a completed respiratory questionnaire and valid spirometric data were included in the analysis (n=13 259). CB, place of birth, heritage, occupational exposures and other risk factors were based on standardised questionnaires. The prevalence of CB was estimated using survey logistic regression-conditional marginal analysis.

RESULTS

The estimated (mean (95% CI)) overall adjusted prevalence of CB was 12.1% (9.3 to 15.6), with a large variation across heritages. Dominican heritage had a fivefold higher prevalence than South American heritage. US-born participants had a higher adjusted prevalence than their non-US-born counterparts (16.8% (12.5 to 22.1) vs 11.0% (8.5 to 14.10); p=0.022). Compared with non-exposed participants, those exposed to cleaning or disinfecting solutions had a higher adjusted prevalence of CB (12.6% (9.1 to 17.1) vs 11.8% (9.2 to 15.1); p=0.024).

CONCLUSIONS

The prevalence of CB was higher among Dominicans than other Hispanic/Latino heritages. CB was more prevalent among US-born participants and those exposed to cleaning and disinfecting solutions.

Genetic ancestry does not explain increased atopic dermatitis susceptibility or worse disease control among African American subjects in 2 large US cohorts

BACKGROUND

Atopic dermatitis (AD) is more common among African American children. Whether there are racial/ethnic difference among adults with AD and the causes for those disparities are unclear.

OBJECTIVE

We sought to examine the relationship between self-reported race/ethnicity and AD and determine whether African genetic ancestry is predictive of these outcomes among African American subjects.

METHODS

We analyzed data from 2 independent multiethnic longitudinal studies: 86,893 subjects aged 18 to 100 years from the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and 5467 subjects aged 2 to 26 years from the national Pediatric Eczema Elective Registry (PEER) cohort. The primary outcomes were physician-diagnosed AD in GERA and repeated measures of self-reported disease control among patients with physician-diagnosed AD at 6-month intervals in PEER. We examined whether self-identified African American race/ethnicity was predictive of these outcomes and then tested whether a continuous measure of African genetic ancestry was associated with outcomes within the African American group.

RESULTS

AD was more common among self-identified African American subjects than non-Hispanic white subjects in GERA (4.4% vs 2.1%; odds ratio, 2.06; 95% CI, 1.70-2.48) and less well-controlled in PEER subjects (odds of 1-level worse control, 1.91; 95% CI, 1.64-2.22). However, African genetic ancestry was not associated with AD risk or control among self-identified African American subjects in either cohort, nor did an AD polygenic risk score or genetic skin pigment score explain the AD disparities in patients with AD.

CONCLUSION

Ancestry-related genetic effects do not explain increased AD prevalence or poorer disease control among African American subjects.

Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans

African Americans (AAs) are an admixed population with widely varying proportion of West African ancestry (WAA). Here we report the correlation of WAA to gene expression and DNA methylation in AA-derived hepatocytes, a cell type important in disease and drug response. We perform mediation analysis to test whether methylation is a mediator of the effect of ancestry on expression. GTEx samples and a second cohort are used as validation. One hundred and thirty-one genes are associated with WAA (FDR < 0.10), 28 of which replicate and represent 220 GWAS phenotypes. Among PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19, and P2RY1 nominally associate with WAA (p < 0.05). We find 1037 WAA-associated, differentially methylated regions (FDR < 0.05), with hypomethylated genes enriched in drug-response pathways. In conclusion, WAA contributes to variability in hepatocyte expression and DNA methylation with identified genes previously implicated for diseases disproportionately affecting AAs, including cardiovascular (PTGIS, PLAT) and renal (APOL1) disease, and drug response (CYP2C19).

Factors affecting spirometry reference range in growing children

OBJECTIVES

To find out the association of weight, height and age with spirometry variables and to generate a regression equation by taking weight as an independent variable beside age and height among children and adolescents of Karachi.

METHODS

A modified form of ISSAC questionnaire was used. The spirometry variables recorded were Forced vital capacity (FVC), Forced expiratory volume in 1 second (FEV1), FEV1/FVC, Peak expiratory flow rate (PEF), Forced expiratory flow between 25% and 75% expired volume (FEF25-75). A person's correlation coefficient among boys and girls were calculated for all spirometry variable considering age, height and weight as independent variables. The linear regression models were calculated.

RESULTS

The results reported a linear correlation of lung function variables with all three independent variables (i.e. p-value = 0.000), in which age and height manifested a strong positive correlation while weight reported a moderately significant correlation. All spirometry variables such as FVC, FEV1, PEF and FEF25-75 reported a significant coefficient of dependency and coefficient of correlation individually with age, height and weight.

CONCLUSION

It is concluded that beside age, height and weight both also have significant correlation with lung volumes so these should be taken into account when using spirometry as a diagnostic test.

Does Salivary Telomere Length Explain Race/Ethnic Differences in Aging?

Telomere length (TL) is a biomarker that can be used to characterize variability in aging and may explain race/ethnic differences in aging. Yet, it remains unclear if TL is related to aging-associated health risks in multi-ethnic populations or if it explains race/ethnic differences in health. We examine whether salivary TL (STL) explains any of the race/ethnic variability in 15 indicators of high-risk biological, physical and cognitive health among 4,074 white, black, and Latinx older adults ages 54+ in the 2008 Health and Retirement Study. TL was assayed from saliva using quantitative PCR (T/S ratio). Decomposition analyses from logistic regression models show variation in STL does not account for any of the observed race/ethnic differences health. In age-adjusted, race-stratified models, STL was associated with HDL, total cholesterol, and lung function among whites, but was not associated with any markers of health among black or Latinx groups. In this diverse national sample of older adults, STL does not account for race/ethnic differences in late life health, is associated with relatively few indicators of health among whites, and is not associated with indicators of health among black or Latinx groups. STL may not be a useful biomarker for understanding racial/ethnic differences in population aging among older adults.

Step-Up Therapy in Black Children and Adults with Poorly Controlled Asthma

BACKGROUND

Morbidity from asthma is disproportionately higher among black patients than among white patients, and black patients constitute the minority of participants in trials informing treatment. Data indicate that patients with inadequately controlled asthma benefit more from addition of a long-acting beta-agonist (LABA) than from increased glucocorticoids; however, these data may not be informative for treatment in black patients.

METHODS

We conducted two prospective, randomized, double-blind trials: one involving children and the other involving adolescents and adults. In both trials, the patients had at least one grandparent who identified as black and had asthma that was inadequately controlled with low-dose inhaled glucocorticoids. We compared combinations of therapy, which included the addition of a LABA (salmeterol) to an inhaled glucocorticoid (fluticasone propionate), a step-up to double to quintuple the dose of fluticasone, or both. The treatments were compared with the use of a composite measure that evaluated asthma exacerbations, asthma-control days, and lung function; data were stratified according to genotypic African ancestry.

RESULTS

When quintupling the dose of fluticasone (to 250 μg twice a day) was compared with adding salmeterol (50 μg twice a day) and doubling the fluticasone (to 100 μg twice a day), a superior response occurred in 46% of the children with quintupling the fluticasone and in 46% of the children with doubling the fluticasone and adding salmeterol (P = 0.99). In contrast, more adolescents and adults had a superior response to added salmeterol than to an increase in fluticasone (salmeterol-low-dose fluticasone vs. medium-dose fluticasone, 49% vs. 28% [P = 0.003]; salmeterol-medium-dose fluticasone vs. high-dose fluticasone, 49% vs. 31% [P = 0.02]). Neither the degree of African ancestry nor baseline biomarkers predicted a superior response to specific treatments. The increased dose of inhaled glucocorticoids was associated with a decrease in the ratio of urinary cortisol to creatinine in children younger than 8 years of age.

CONCLUSIONS

In contrast to black adolescents and adults, almost half the black children with poorly controlled asthma had a superior response to an increase in the dose of an inhaled glucocorticoid and almost half had a superior response to the addition of a LABA. (Funded by the National Heart, Lung, and Blood Institute; BARD ClinicalTrials.gov number, NCT01967173.).

Exacerbation-prone asthma in the context of race and ancestry in Asthma Clinical Research Network trials

BACKGROUND

Minority groups of African descent experience disproportionately greater asthma morbidity compared with other racial groups, suggesting that genetic variation from a common ancestry could influence exacerbation risk.

OBJECTIVE

We evaluated clinical trial measures in the context of self-reported race and genetic ancestry to identify risk factors for asthma exacerbations.

METHODS

One thousand eight hundred forty multiethnic subjects from 12 Asthma Clinical Research Network and AsthmaNet trials were analyzed for incident asthma exacerbations with Poisson regression models that included clinical measures, self-reported race (black, non-Hispanic white, and other), and estimates of global genetic African ancestry in a subgroup (n = 760).

RESULTS

Twenty-four percent of 1840 subjects self-identified as black. Black and white subjects had common risk factors for exacerbations, including a history of 2 or more exacerbations in the previous year and FEV₁ percent predicted values, whereas chronic sinusitis, allergic rhinitis, and gastroesophageal reflux disease were only associated with increased exacerbation risk in black subjects. In the combined multiethnic cohort, neither race (P = .30) nor percentage of genetic African ancestry as a continuous variable associated with exacerbation risk (adjusted rate ratio [RR], 1.26 [95% CI, 0.94-1.70; P = .13]; RR per 1-SD change [32% ancestry], 0.97 [95% CI, 0.78-1.19; P = .74]). However, in 161 black subjects with genetic data, those with African ancestry greater than the median (≥82%) had a significantly greater risk of exacerbation (RR, 3.06 [95% CI, 1.09-8.6; P = .03]).

CONCLUSION

Black subjects have unique risk factors for asthma exacerbations, of which global African genetic ancestry had the strongest effect.

Ambient air pollution, asthma drug response, and telomere length in African American youth

BACKGROUND

Telomere length (TL) can serve as a potential biomarker for conditions associated with chronic oxidative stress and inflammation, such as asthma. Air pollution can induce oxidative stress. Understanding the relationship between TL, asthma, and air pollution is important for identifying risk factors contributing to unhealthy aging in children.

OBJECTIVES

We sought to investigate associations between exposures to ambient air pollutants and TL in African American children and adolescents and to examine whether African ancestry, asthma status, and steroid medication use alter the association.

METHODS

Linear regression was used to examine associations between absolute telomere length (aTL) and estimated annual average residential ozone (O3) and fine particulate matter with a diameter of 2.5 μm or less (PM2.5) exposures in a cross-sectional analysis of 1072 children in an existing asthma case-control study. African ancestry, asthma status, and use of steroid medications were examined as effect modifiers.

RESULTS

Participants' aTLs were measured by using quantitative PCR. A 1-ppb and 1 μg/m3 increase in annual average exposure to O3 and PM2.5 were associated with a decrease in aTL of 37.1 kilo-base pair (kb; 95% CI, -66.7 to -7.4 kb) and 57.1 kb (95% CI, -118.1 to 3.9 kb), respectively. African ancestry and asthma were not effect modifiers; however, exposure to steroid medications modified the relationships between TL and pollutants. Past-year exposure to O3 and PM2.5 was associated with shorter TLs in patients without steroid use.

CONCLUSION

Exposure to air pollution was associated with shorter TLs in nonasthmatic children and adolescents. This was not the case for asthmatic children as a group, but those receiving steroid medication had less shortening than those not using steroids. Reduced exposure to air pollution in childhood might help to preserve TL.

Global Lung Function Initiative-2012 'other/mixed' spirometry reference equation provides the best overall fit for Australian Aboriginal and/or Torres Strait Islander children and young adults

BACKGROUND AND OBJECTIVE

Ethnic-specific reference equations are recommended when performing spirometry. In the absence of appropriate reference equations for Australian Aboriginal and/or Torres Strait Islanders (Indigenous), we determined whether any of the existing Global Lung Function Initiative (GLI)-2012 equations were suitable for use in Indigenous children/young adults.

METHODS

We performed spirometry on 1278 participants (3-25 years) who were identified as Aboriginal, Torres Strait Islander or 'both'. Questionnaires and medical records were used to identify 'healthy' participants. GLI2012_DataConversion software was used to apply the 'Caucasian', 'African-American' and 'other/mixed' equations.

RESULTS

We included 930 healthy participants. Mean z-scores for forced expiratory volume in 1 s (FEV₁ ) and forced vital capacity (FVC) were lower than the Caucasian predicted values (range: -0.53 to -0.60) and higher than African-American (range: 0.70 to 0.78) but similar to other/mixed (range: 0.00 to 0.08). The distribution of healthy participants around the upper and lower limits of normal (~5%) fit well for the other/mixed equation compared to the Caucasian and African-American equations.

CONCLUSION

Of the available GLI-2012 reference equations, the other/mixed reference equation provides the best overall fit for Indigenous Australian children and young adults (3-25 years). Healthy data from additional communities and adults around Australia will be required to confirm generalizability of findings.

Prevalence and correlates of chronic obstructive pulmonary disease and chronic respiratory symptoms in rural southwestern Uganda: a cross-sectional, population-based study

Background

The global burden of chronic obstructive pulmonary disease (COPD) disproportionately affects resource-limited settings such as sub-Saharan Africa (SSA), but population-based prevalence estimates in SSA are rare. We aimed to estimate the population prevalence of COPD and chronic respiratory symptoms in rural southwestern Uganda.

Methods

Adults at least 18 years of age who participated in a population-wide census in rural southwestern Uganda completed respiratory questionnaires and lung function testing with bronchodilator challenge at health screening events in June 2015. We defined COPD as post-bronchodilator forced expiratory volume in one second to forced vital capacity ratio less than the lower limit of normal. We fit multivariable linear and log binomial regression models to estimate correlates of abnormal lung function and respiratory symptoms, respectively. We included inverse probability of sampling weights in models to facilitate population-level estimates.

Results

Forty-six percent of census participants (843/1814) completed respiratory questionnaires and spirometry, of which 565 (67%) met acceptability standards. COPD and respiratory symptom population prevalence were 2% (95% confidence interval (CI)  = 1%-3%) and 30% (95% CI = 25%-36%), respectively. Respiratory symptoms were more prevalent and lung function was lower among women and ever-smokers (P < 0.05). HIV serostatus was associated with neither respiratory symptoms nor lung function.

Conclusions

COPD population prevalence was low despite prevalent respiratory symptoms. This work adds to the growing body of literature depicting lower-than-expected COPD prevalence estimates in SSA and raises questions about whether the high respiratory symptom burden in rural southwestern Uganda represents underlying structural lung disease not identified by screening spirometry.

Discriminative Accuracy of FEV1:FVC Thresholds for COPD-Related Hospitalization and Mortality

Importance

According to numerous current guidelines, the diagnosis of chronic obstructive pulmonary disease (COPD) requires a ratio of the forced expiratory volume in the first second to the forced vital capacity (FEV1:FVC) of less than 0.70, yet this fixed threshold is based on expert opinion and remains controversial.

Objective

To determine the discriminative accuracy of various FEV1:FVC fixed thresholds for predicting COPD-related hospitalization and mortality.

Design, Setting, and Participants

The National Heart, Lung, and Blood Institute (NHLBI) Pooled Cohorts Study harmonized and pooled data from 4 US general population-based cohorts (Atherosclerosis Risk in Communities Study; Cardiovascular Health Study; Health, Aging, and Body Composition Study; and Multi-Ethnic Study of Atherosclerosis). Participants aged 45 to 102 years were enrolled from 1987 to 2000 and received follow-up longitudinally through 2016.

Exposures

Presence of airflow obstruction, which was defined by a baseline FEV1:FVC less than a range of fixed thresholds (0.75 to 0.65) or less than the lower limit of normal as defined by Global Lung Initiative reference equations (LLN).

Main Outcomes and Measures

The primary outcome was a composite of COPD hospitalization and COPD-related mortality, defined by adjudication or administrative criteria. The optimal fixed FEV1:FVC threshold was defined by the best discrimination for these COPD-related events as indexed using the Harrell C statistic from unadjusted Cox proportional hazards models. Differences in C statistics were compared with respect to less than 0.70 and less than LLN thresholds using a nonparametric approach.

Results

Among 24 207 adults in the pooled cohort (mean [SD] age at enrollment, 63 [10.5] years; 12 990 [54%] women; 16 794 [69%] non-Hispanic white; 15 181 [63%] ever smokers), complete follow-up was available for 11 077 (77%) at 15 years. During a median follow-up of 15 years, 3925 participants experienced COPD-related events over 340 757 person-years of follow-up (incidence density rate, 11.5 per 1000 person-years), including 3563 COPD-related hospitalizations and 447 COPD-related deaths. With respect to discrimination of COPD-related events, the optimal fixed threshold (0.71; C statistic for optimal fixed threshold, 0.696) was not significantly different from the 0.70 threshold (difference, 0.001 [95% CI, -0.002 to 0.004]) but was more accurate than the LLN threshold (difference, 0.034 [95% CI, 0.028 to 0.041]). The 0.70 threshold provided optimal discrimination in the subgroup analysis of ever smokers and in adjusted models.

Conclusions and Relevance

Defining airflow obstruction as FEV1:FVC less than 0.70 provided discrimination of COPD-related hospitalization and mortality that was not significantly different or was more accurate than other fixed thresholds and the LLN. These results support the use of FEV1:FVC less than 0.70 to identify individuals at risk of clinically significant COPD.

Minimum sample size for developing a multivariable prediction model: Part I - Continuous outcomes

In the medical literature, hundreds of prediction models are being developed to predict health outcomes in individuals. For continuous outcomes, typically a linear regression model is developed to predict an individual's outcome value conditional on values of multiple predictors (covariates). To improve model development and reduce the potential for overfitting, a suitable sample size is required in terms of the number of subjects (n) relative to the number of predictor parameters (p) for potential inclusion. We propose that the minimum value of n should meet the following four key criteria: (i) small optimism in predictor effect estimates as defined by a global shrinkage factor of ≥0.9; (ii) small absolute difference of ≤ 0.05 in the apparent and adjusted R2 ; (iii) precise estimation (a margin of error ≤ 10% of the true value) of the model's residual standard deviation; and similarly, (iv) precise estimation of the mean predicted outcome value (model intercept). The criteria require prespecification of the user's chosen p and the model's anticipated R2 as informed by previous studies. The value of n that meets all four criteria provides the minimum sample size required for model development. In an applied example, a new model to predict lung function in African-American women using 25 predictor parameters requires at least 918 subjects to meet all criteria, corresponding to at least 36.7 subjects per predictor parameter. Even larger sample sizes may be needed to additionally ensure precise estimates of key predictor effects, especially when important categorical predictors have low prevalence in certain categories.

Spirometry reference values for Black adults in Brazil

Objective:

To derive reference equations for spirometry in healthy Black adult never smokers in Brazil, comparing them with those published in 2007 for White adults in the country.

Methods:

The examinations followed the standards recommended by the Brazilian Thoracic Association, and the spirometers employed met the technical requirements set forth in the guidelines of the American Thoracic Society/European Respiratory Society. The lower limits were defined as the 5th percentile of the residuals.

Results:

Reference equations and limits were derived from a sample of 120 men and 124 women, inhabitants of eight Brazilian cities, all of whom were evaluated with a flow spirometer. The predicted values for FVC, FEV₁, FEV₁/FVC ratio, and PEF were better described by linear equations, whereas the flows were better described by logarithmic equations. The FEV₁ and FVC reference values derived for Black adults were significantly lower than were those previously derived for White adults, regardless of gender.

Conclusions:

The fact that the predicted spirometry values derived for the population of Black adults in Brazil were lower than those previously derived for White adults in the country justifies the use of an equation specific to the former population.

Acculturation is associated with asthma burden and pulmonary function in Latino youth: The GALA II study

BACKGROUND

Acculturation is an important predictor of asthma in Latino youth, specifically Mexican Americans. Less is known about acculturation and pulmonary function measures.

OBJECTIVE

We sought to estimate the association of acculturation measures with asthma and pulmonary function in Latino youth and determine whether this association varies across Latino subgroups.

METHODS

We included 1849 Latinos (302 Caribbean Spanish, 193 Central or South Americans, 1136 Mexican Americans, and 218 other Latino children) aged 8 to 21 years from 4 urban regions in the United States. Acculturation measures include nativity status, age of immigration, language of preference, and generation in the United States. We used multivariable logistic and linear regression models to quantify the association of acculturation factors with the presence of asthma (case-control study) and pulmonary function (case-only study), adjusting for demographic, socioenvironmental, and clinical variables.

RESULTS

For all acculturation measures (nativity status, age of immigration, language of preference, and generation in the United States), greater levels of acculturation were associated with greater odds of asthma. Among cases, high (English preference) and medium (equal preference for Spanish and English) levels of language acculturation were associated with decreased bronchodilator response compared with low (Spanish preference) levels (P = .009 and .02, respectively). Similarly, high language acculturation was associated with increased FEV₁ compared with low language acculturation (P = .02). There was insufficient evidence of heterogeneity for associations across Latino subgroups.

CONCLUSIONS

Acculturation was associated with diagnosed asthma and pulmonary function in Latino children and is an important factor to consider in the management of Latino youth with asthma.

High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report

High-throughput, "next-generation" sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.

Association of African Ancestry With Electrocardiographic Voltage and Concentric Left Ventricular Hypertrophy: The Dallas Heart Study

Importance

Compared with white individuals, black individuals have increased electrocardiographic voltage and an increased prevalence of concentric left ventricular (LV) hypertrophy. Whether environmental or genetic factors lead to these racial differences is unknown.

Objective

To determine whether proportion of genetically determined African ancestry among self-reported black individuals is associated with increased electrocardiographic voltage and concentric LV hypertrophy (LVH).

Design, Setting, and Participants

The Dallas Heart Study is a probability-based cohort study of English- or Spanish-speaking Dallas County, Texas, residents, with deliberate oversampling of black individuals. Participants underwent extensive phenotyping, which included electrocardiography (ECG), cardiac magnetic resonance imaging (CMR), and dual-energy radiography absorptiometry (DEXA) at a single center. Participants aged 18 to 65 years who enrolled in the Dallas Heart Study between July 2000 and December 2002, self-identified as black (n = 1251) or white (n = 826), and had ECG, CMR, and DEXA data were included in this analysis. Data were analyzed from June 2017 to September 2018.

Exposures

Proportion of African ancestry.

Main Outcomes and Measures

Electrocardiographic voltage (12-lead and 9-lead) and markers of concentric LVH as assessed by CMR (LV concentricity0.67 [LV mass/end-diastolic volume0.67], LV wall thickness [LVWT], and prevalent LVH [defined by LV mass/height2.7]).

Results

Of the 2077 participants included in the study, 1138 (54.8%) were women, and the mean (SD) age was 45.2 (9.9) years. Black race and African ancestry were individually associated with increased ECG voltage, LV concentricity0.67, LVWT, and prevalent LVH in multivariable analyses adjusting for age, sex, systolic blood pressure, antihypertensive medication use, and body composition. When African ancestry and black race were entered together into multivariable models, African ancestry but not black race remained associated with ECG voltage, LVWT, LV concentricity0.67, and prevalent LVH. Among black participants, African ancestry remained associated with these 4 phenotypes (12-lead voltage: β, 0.05; P = .04; LVWT: β, 0.05; P = .02; LV concentricty0.67: β, 0.05; P = .045; prevalent LVH: odds ratio, 1.2; 95% CI, 1.03-1.4; P = .02).

Conclusions and Relevance

Genetically determined African ancestry was associated with electrocardiographic voltage, measures of concentric LV remodeling, and prevalent LVH. These data support a genetic basis related to African ancestry for the increased prevalence of these cardiovascular traits in black individuals.

Secondhand smoke exposure and asthma outcomes among African-American and Latino children with asthma

BACKGROUND

Secondhand smoke (SHS) exposures have been linked to asthma-related outcomes but quantitative dose-responses using biomarkers of exposure have not been widely reported.

OBJECTIVES

Assess dose-response relationships between plasma cotinine-determined SHS exposure and asthma outcomes in minority children, a vulnerable population exposed to higher levels of SHS and under-represented in the literature.

METHODS

We performed analyses in 1172 Latino and African-American children with asthma from the mainland USA and Puerto Rico. We used logistic regression to assess relationships of cotinine levels ≥0.05 ng/mL with asthma exacerbations (defined as asthma-related hospitalisations, emergency room visits or oral steroid prescription) in the previous year and asthma control. The shape of dose-response relationships was assessed using a continuous exposure variable in generalised additive logistic models with penalised splines.

RESULTS

The OR for experiencing asthma exacerbations in the previous year for cotinine levels ≥0.05 ng/mL, compared with <0.05 ng/mL, was 1.40 (95% CI 1.03 to 1.89), while the OR for poor asthma control was 1.53 (95% CI 1.12 to 2.13). Analyses for dose-response relationships indicated increasing odds of asthma outcomes related with increasing exposure, even at cotinine levels associated with light SHS exposures.

CONCLUSIONS

Exposure to SHS was associated with higher odds of asthma exacerbations and having poorly controlled asthma with an increasing dose-response even at low levels of exposure. Our results support the conclusion that there are no safe levels of SHS exposures.

Racial Disparities in Lung Cancer Survival: The Contribution of Stage, Treatment, and Ancestry

INTRODUCTION

Lung cancer is a leading cause of cancer-related death worldwide. Racial disparities in lung cancer survival exist between blacks and whites, yet they are limited by categorical definitions of race. We sought to examine the impact of African ancestry on overall survival among blacks and whites with NSCLC cases.

METHODS

Incident cases of NSCLC in blacks and whites from the prospective Southern Community Cohort Study (N = 425) were identified through linkage with state cancer registries in 12 southern states. Vital status was determined by linkage with the National Death Index and Social Security Administration. We evaluated the impact of African ancestry (as estimated by using genome-wide ancestry-informative markers) on overall survival by calculating the time-dependent area under the curve (AUC) for Cox proportional hazards models, adjusting for relevant covariates such as stage and treatment. We replicated our findings in an independent population of NSCLC cases in blacks.

RESULTS

Global African ancestry was not significantly associated with overall survival among NSCLC cases. There was no change in model performance when Cox proportional hazards models with and without African ancestry were compared (AUC = 0.79 for each model). Removal of stage and treatment reduced the average time-dependent AUC from 0.79 to 0.65. Similar findings were observed in our replication study.

CONCLUSIONS

Stage and treatment are more important predictors of survival than African ancestry is. These findings suggest that racial disparities in lung cancer survival may disappear with similar early detection efforts for blacks and whites.

African ancestry is associated with cluster-based childhood asthma subphenotypes

BACKGROUND

Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse sample of asthmatic children and to assess subphenotype-specific genetic ancestry in African-American asthmatic children.

METHODS

A total of 1211 asthmatic children including 813 in the Childhood Asthma Management Program and 398 in the Childhood Asthma Research and Education program were studied. Unsupervised cluster analysis on clinical phenotypes was conducted to identify homogeneous subphenotypes. Subphenotype-specific genetic ancestry was estimated for 167 African-American asthmatic children. Genetic ancestry association with subphenotypes/clinical phenotypes were determined.

RESULTS

Three distinct subphenotypes were identified: a moderate atopic dermatitis (AD) group with negative skin prick test (SPT) and preserved lung function; a high AD group with positive SPT and airway hyperresponsiveness; and a low AD group with positive SPT and lower lung function. African ancestry at asthma genome-wide association study (GWAS) SNPs differed between subphenotypes (64, 89, and 94% for the three subphenotypes, respectively) and was inversely correlated with AD; each additional 10% increase in African ancestry was associated with 1.5 fold higher in IgE and 6.3 higher odds of positive SPT (all p-values < 0.0001).

CONCLUSIONS

By conducting phenotype-based cluster analysis and assessing subphenotype-specific genetic ancestry, we were able to identify homogeneous subphenotypes for childhood asthma that showed significant variation in genetic ancestry of African-American asthmatic children. This finding demonstrates the utility of these complementary approaches to understand and refine childhood asthma subphenotypes and enable more targeted therapy.

West African Ancestry and Nocturnal Blood Pressure in African Americans: The Jackson Heart Study

BACKGROUND

African Americans have a higher prevalence of nocturnal hypertension and nondipping blood pressure than European Americans, but the genetic contribution to these racial differences remains unclear. We assessed the association of the percentage West African genetic ancestry with nocturnal hypertension and nondipping blood pressure in 932 African Americans from the Jackson Heart Study.

METHODS

Using percentage West African ancestry determined from 389 ancestry informative markers, participants were categorized into tertiles (tertile 1 [low]: <79.3%, tertile 2: ≥79.3-86.3%, and tertile 3 [high]: >86.3%). Nocturnal hypertension was defined as mean nighttime (midnight-6 am) systolic (SBP)/diastolic blood pressure ≥120/70 mm Hg. Nondipping blood pressure was defined as mean nighttime-to-daytime (10 am-8 pm) SBP ratio >0.90.

RESULTS

Nocturnal hypertension was present in 57.9% of participants; 66.6% had nondipping blood pressure. The mean age was 59.4 years, 32.8% were male, and 56.0% were taking antihypertensive medication. The prevalence ratios (95% confidence interval) adjusted for age, sex, cardiovascular disease risk factors, and socioeconomic and psychosocial factors comparing participants with moderate and high to those with low percentage West African ancestry for nocturnal hypertension were 0.98 (0.87-1.10) and 0.95 (0.84-1.08), respectively, and for nondipping blood pressure was 0.96 (0.86-1.07) and 0.98 (0.88-1.09), respectively.

CONCLUSIONS

West African ancestry was not associated with nocturnal hypertension and nondipping blood pressure among African Americans. While rare genetic variants cannot be ruled out, these data highlight the need to better understand how environmental and behavioral factors contribute to differences in nocturnal blood pressure among African Americans compared with European Americans.

An American Thoracic Society/National Heart, Lung, and Blood Institute Workshop Report: Addressing Respiratory Health Equality in the United States

Health disparities related to race, ethnicity, and socioeconomic status persist and are commonly encountered by practitioners of pediatric and adult pulmonary, critical care, and sleep medicine in the United States. To address such disparities and thus progress toward equality in respiratory health, the American Thoracic Society and the National Heart, Lung, and Blood Institute convened a workshop in May of 2015. The workshop participants addressed health disparities by focusing on six topics, each of which concluded with a panel discussion that proposed recommendations for research on racial, ethnic, and socioeconomic disparities in pulmonary, critical care, and sleep medicine. Such recommendations address best practices to advance research on respiratory health disparities (e.g., characterize broad ethnic groups into subgroups known to differ with regard to a disease of interest), risk factors for respiratory health disparities (e.g., study the impact of new tobacco or nicotine products on respiratory diseases in minority populations), addressing equity in access to healthcare and quality of care (e.g., conduct longitudinal studies of the impact of the Affordable Care Act on respiratory and sleep disorders), the impact of personalized medicine on disparities research (e.g., implement large studies of pharmacogenetics in minority populations), improving design and methodology for research studies in respiratory health disparities (e.g., use study designs that reduce participants' burden and foster trust by engaging participants as decision-makers), and achieving equity in the pulmonary, critical care, and sleep medicine workforce (e.g., develop and maintain robust mentoring programs for junior faculty, including local and external mentors). Addressing these research needs should advance efforts to reduce, and potentially eliminate, respiratory, sleep, and critical care disparities in the United States.

Collating Spirometry reference values in Asian children and Adolescents; puzzle out the reasons for variations

Lung function tests are essential for the diagnosis and management of different respiratory tract diseases; among them the spirometry is the gold standard technique. The accurate diagnosis, management and monitoring require proper interpretation of the results which depends upon the availability of spirometry reference data for that particular region to differentiate the diseased condition from the normal ones. Multiple studies had been done to find out their own area specific reference ranges but it is still lacking. This need was fulfilled by the Global Lung Function Initiative (GLI) in 2012, which reported the first global spirometry equation for all of the age groups. But some of the studies reported difference among GLI reference range and the measured range for that particular region. So here is the review of the reference ranges among 35,603 Asian children and adolescents from the 32 studies done specifically in Asia. The aim was to compare them with the study done by GLI team, along with these, tried to rule out the causal factor that are responsible for the variations in the reference ranges among the children and adolescents of different population. The literature was searched by using Google scholar and PubMed during the month of March up to July 2017. The review of all the articles published in Asia, specifically accounting for normal reference ranges in children and adolescent exhibit a wide variation among the reference ranges. This also suggest involvement of multiple modifiable and non-modifiable risk factors. So it's necessary to update the reference ranges for spirometry and its prediction equation as well.

An ancestry-based approach for detecting interactions

BACKGROUND

Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies.

RESULTS

In this work, we develop a new statistical approach to address these issues that leverages genetic ancestry, defined as the proportion of ancestry derived from each ancestral population (e.g., the fraction of European/African ancestry in African Americans), in admixed populations. We applied our method to gene expression and methylation data from African American and Latino admixed individuals, respectively, identifying nine interactions that were significant at P<5×10-8. We show that two of the interactions in methylation data replicate, and the remaining six are significantly enriched for low P-values (P<1.8×10-6).

CONCLUSION

We show that genetic ancestry can be a useful proxy for unknown and unmeasured covariates in the search for interaction effects. These results have important implications for our understanding of the genetic architecture of complex traits.

Neighborhood Perceptions and Cumulative Impacts of Low Level Chronic Exposure to Fine Particular Matter (PM2.5) on Cardiopulmonary Health

Adverse perceptions of neighborhood safety, aesthetics and quality including access to resources can induce stress and may make individuals more sensitive to cardiopulmonary effects of air pollution exposure. Few studies have examined neighborhood perceptions as important and modifiable non-chemical stressors of the built environment that may exacerbate effects of air pollution on cardiopulmonary health outcomes, particularly among general population based cohorts. This study examined associations between low-level chronic exposure to fine particulate matter (PM2.5) and cardiopulmonary health, and the potential mediating or modifying effects of adverse neighborhood perceptions. Using data from the Survey of the Health of Wisconsin (SHOW), 2230 non-asthmatic adults age 21-74 were included in the analyses. The overall goals of this study were to assess if individuals who experience stress from neighborhood environments in which they live were more sensitive to low levels of fine particular matter (PM2.5 μg/m³). Demographic predictors of air pollution exposure included younger age, non-White race, lower education and middle class income. After adjustments, objective lung function measures (FEV1 and FEV1 to FVC ratio) were the only cardiopulmonary health indicators significantly associated with chronic three-year annual averages of PM2.5. Among all non-asthmatics, a ten unit increase in estimated three year annual average PM2.5 exposure was significantly associated with lower forced expiratory volume (L) in one second FEV1 (β = -0.40 μg/L; 95% CI -0.45, -0.06). Among all individuals, adverse perceptions of the neighborhood built environment did not appear to statistically moderate or mediate associations. However, stratified analysis did reveal significant associations between PM2.5 and lung function (FEV1) only among individuals with negative perceptions and increased reports of neighborhood stressors. These findings included individuals who felt their neighborhoods were poorly maintained (β = -0.82; 95% CI -1.35, -0.28), experienced stress from crime (β = -0.45; 95% CI -0.94, 0.04) or reported neighborhood is not well maintained (β = -1.13, CI -2.04, -0.24). These significant associations were similar for FEV1 to FVC ratio. Multi-pronged approaches addressing both neighborhood built environment aesthetics and air pollution regulation may be necessary to protect vulnerable and susceptible individuals and reduce persistent inequalities.

Gene editing as a promising approach for respiratory diseases

Respiratory diseases, which are leading causes of mortality and morbidity in the world, are dysfunctions of the nasopharynx, the trachea, the bronchus, the lung and the pleural cavity. Symptoms of chronic respiratory diseases, such as cough, sneezing and difficulty breathing, may seriously affect the productivity, sleep quality and physical and mental well-being of patients, and patients with acute respiratory diseases may have difficulty breathing, anoxia and even life-threatening respiratory failure. Respiratory diseases are generally heterogeneous, with multifaceted causes including smoking, ageing, air pollution, infection and gene mutations. Clinically, a single pulmonary disease can exhibit more than one phenotype or coexist with multiple organ disorders. To correct abnormal function or repair injured respiratory tissues, one of the most promising techniques is to correct mutated genes by gene editing, as some gene mutations have been clearly demonstrated to be associated with genetic or heterogeneous respiratory diseases. Zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) systems are three innovative gene editing technologies developed recently. In this short review, we have summarised the structure and operating principles of the ZFNs, TALENs and CRISPR/Cas9 systems and their preclinical and clinical applications in respiratory diseases.

Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

Background

Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance.

Results

We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity.

Conclusion

Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks.

Electronic supplementary material

The online version of this article (10.1186/s12863-017-0570-y) contains supplementary material, which is available to authorized users.

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases

Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations.

Spirometry Reference Equations from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos)

RATIONALE

Accurate reference values for spirometry are important because the results are used for diagnosing common chronic lung diseases such as asthma and chronic obstructive pulmonary disease, estimating physiologic impairment, and predicting all-cause mortality. Reference equations have been established for Mexican Americans but not for others with Hispanic/Latino backgrounds.

OBJECTIVES

To develop spirometry reference equations for adult Hispanic/Latino background groups in the United States.

METHODS

The HCHS/SOL (Hispanic Community Health Study/Study of Latinos) recruited a population-based probability sample of 16,415 Hispanics/Latinos aged 18-74 years living in the Bronx, Chicago, Miami, and San Diego. Participants self-identified as being of Puerto Rican, Cuban, Dominican, Mexican, or Central or South American background. Spirometry was performed using standardized methods with central quality control monitoring. Spirometric measures from a subset of 6,425 never-smoking participants without respiratory symptoms or disease were modeled as a function of sex, age, height, and Hispanic/Latino background to produce background-specific reference equations for the predicted value and lower limit of normal.

MEASUREMENTS AND MAIN RESULTS

Dominican and Puerto Rican Americans had substantially lower predicted and lower limit of normal values for FVC and FEV₁ than those in other Hispanic/Latino background groups and also than Mexican American values from NHANES III (Third National Health and Nutrition Examination Survey).

CONCLUSIONS

For patients of Dominican and Puerto Rican background who present with pulmonary symptoms in clinical practice, use of background-specific spirometry reference equations may provide more appropriate predicted and lower limit of normal values, enabling more accurate diagnoses of abnormality and physiologic impairment.

APOL1 genetic variants are not associated with longitudinal blood pressure in young black adults

Whether APOL1 polymorphisms contribute to the excess risk of hypertension among blacks is unknown. To assess this we evaluated whether self-reported race and, in blacks, APOL1 risk variants (high-risk [2 risk alleles] versus low-risk [0-1 risk allele]) were associated with longitudinal blood pressure. Blood pressure trajectories were determined using linear mixed-effects (slope) and latent class models (5 distinct groups) during 25 years of follow-up in the Coronary Artery Risk Development in Young Adults Study. Associations of race and APOL1 genotypes with blood pressure change, separately, using linear mixed-effects and multinomial logistic regression models, adjusting for demographic, socioeconomic, and traditional hypertension risk factors, anti-hypertensive medication use, and kidney function were evaluated. Among 1700 whites and 1330 blacks (13% APOL1 high-risk, mean age 25 years; 46% male) mean mid-, ([systolic + diastolic blood pressure]/2), systolic, and diastolic blood pressures were 89, 110, and 69 mm Hg, respectively. One percent of participants used anti-hypertensive medications at baseline. Compared to whites, blacks, regardless of APOL1 genotype, had significantly greater increases in mid-blood pressure and were more likely to experience significantly increasing mid-blood pressure trajectories with adjusted relative risk ratios of 5.21 and 7.27 for moderate-increasing and elevated-increasing versus low-stable blood pressure, respectively. Among blacks, longitudinal mid-blood pressure changes and mid-blood pressure trajectory classification were similar by APOL1 risk status. Modeling systolic and diastolic blood pressure as outcomes yielded similar findings. From young adulthood to mid-life, blacks have greater blood pressure increases versus whites that are not fully explained by traditional risk factors. Thus APOL1 variants are not associated with longitudinal blood pressure in blacks.

Breastfeeding associated with higher lung function in African American youths with asthma

OBJECTIVE

In the United States, Puerto Ricans and African Americans have lower prevalence of breastfeeding and worse clinical outcomes for asthma compared with other racial/ethnic groups. We hypothesize that the history of breastfeeding is associated with increased forced expiratory volume in 1 second (FEV1) % predicted and reduced asthma exacerbations in Latino and African American youths with asthma.

METHODS

As part of the Genes-environments & Admixture in Latino Americans (GALA II) Study and the Study of African Americans, asthma, Genes & Environments (SAGE II), we conducted case-only analyses in children and adolescents aged 8-21 years with asthma from four different racial/ethnic groups: African Americans (n = 426), Mexican Americans (n = 424), mixed/other Latinos (n = 255), and Puerto Ricans (n = 629). We investigated the association between any breastfeeding in infancy and FEV1% predicted using multivariable linear regression; Poisson regression was used to determine the association between breastfeeding and asthma exacerbations.

RESULTS

Prevalence of breastfeeding was lower in African Americans (59.4%) and Puerto Ricans (54.9%) compared to Mexican Americans (76.2%) and mixed/other Latinos (66.9%; p < 0.001). After adjusting for covariates, breastfeeding was associated with a 3.58% point increase in FEV1% predicted (p = 0.01) and a 21% reduction in asthma exacerbations (p = 0.03) in African Americans only.

CONCLUSION

Breastfeeding was associated with higher FEV1% predicted in asthma and reduced number of asthma exacerbations in African American youths, calling attention to continued support for breastfeeding.

Primary Care Physicians' Collection, Comfort, and Use of Race and Ethnicity in Clinical Practice in the United States

Purpose: The clinical utility of race and ethnicity has been debated. It is important to understand if and how race and ethnicity are communicated and collected in clinical settings. We investigated physicians' self-reported methods of collecting a patient's race and ethnicity in the clinical encounter, their comfort with collecting race and ethnicity, and associations with use of race in clinical decision-making.

Methods: A national cross-sectional study of 787 clinically active general internists in the United States. Physicians' self-reported comfort with collecting patient race and ethnicity, their collection practices, and use of race in clinical care were assessed. Bivariate and multivariable regression analyses were conducted to examine associations between comfort, collection practices, and use of race.

Results: Most physicians asked patients to self-report their race or ethnicity (26.5%) on an intake form or collected this information directly from patients (26.2%). Most physicians were comfortable collecting patient race and ethnicity (84.3%). Physicians who were more comfortable collecting patient race and ethnicity (β=1.65; [95% confidence interval; CI 0.03–3.28]) or who directly collected patients' race and ethnicity (β=1.24 [95% CI 0.07–2.41]) were more likely to use race in clinical decision-making than physicians who were uncomfortable.

Conclusions: This study documents variation in physician comfort level and practice patterns regarding patient race and ethnicity data collection. As the U.S. population becomes more diverse, future work should examine how physicians speak about race and ethnicity with patients and their use of race and ethnicity data impact patient–physician relationships, clinical decision-making, and patient outcomes.

Predictors of emergency department use in children with persistent asthma in metropolitan Atlanta, Georgia

BACKGROUND

Racial disparities are evident among children with asthma in the United States, with non-Hispanic black children at particularly high risk for poor asthma outcomes, including frequent emergency department (ED) use for asthma exacerbations.

OBJECTIVE

To compare asthma features in non-Hispanic black vs white children in Atlanta, Georgia, and determine what clinical features predict future ED use for asthma.

METHODS

Self-reported black and white children 6 to 17 years of age with persistent asthma treated with controller medications completed medical history questionnaires, lung function testing, aeroallergen sensitization testing, and venipuncture. Medical records were reviewed for asthma-related ED visits for 12 months after the initial study visit.

RESULTS

A total of 276 children were enrolled. Black children, compared with white children, resided in more disadvantaged zip code areas and were more likely to have public insurance. Black children also had more features of asthma severity and more ED visits during the study period. Predictors of ED use, aside from a previous ED visit, differed by race. After adjustment for socioeconomic status, predictors of ED use in white children included an ED visit in the previous year and sensitization to pets and dust; in black children, predictors included ED use in the previous year, the number of asthma controller medications, forced expiratory volume in 1 second less than 80% predicted, blood eosinophil count greater than 4%, and mold sensitization.

CONCLUSION

Asthma features and ED use differ between black and white children in metropolitan Atlanta. Strategies to eliminate allergen exposure in the home and improve asthma control in these children may require tailoring for different racial groups.

What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression

Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.

Evaluation of the Global Lung Initiative 2012 Reference Values for Spirometry in African Children

RATIONALE

Despite the high burden of respiratory disease, no spirometry reference values for African children are available.

OBJECTIVES

Investigate whether the Global Lung Initiative (GLI-2012) reference values for spirometry are appropriate for children in sub-Saharan Africa and assess the impact of malnutrition on lung function.

METHODS

Anthropometry and spirometry were obtained in children aged 6 to 12 years from urban and semiurban schools in three African countries. Spirometry z-scores were derived using the GLI-2012 prediction equations for African Americans. Thinness (body mass index z-score < -2) was a surrogate for malnutrition. Spirometry outcomes were compared with those of African American children from the third National Health and Nutrition Survey.

MEASUREMENTS AND MAIN RESULTS

Spirometry data were analyzed from 1,082 schoolchildren (51% boys) aged 6.0 to 12.8 years in Angola (n = 306), Democratic Republic of the Congo (n = 377), and Madagascar (n = 399). GLI-2012 provided a good fit with mean (SD) z-scores of -0.11 (0.83) for FEV₁, -0.08 (0.86) for FVC, and -0.07 (0.83) for FEV₁/FVC. Because of low scatter, the fifth centile corresponded to -1.3 z-scores in boys and -1.5 z-scores in girls. Malnourished African children had a normal FEV₁/FVC ratio but significant reductions of ∼0.5 z-scores (∼5%) in FEV₁ and FVC compared with African American peers from the third National Health and Nutrition Survey. Children in Angola had the lowest, and those in Madagascar had the highest, zFEV₁ and zFVC.

CONCLUSIONS

The results of this study support the use of GLI-2012 reference values for schoolchildren in sub-Saharan Africa. Malnutrition affects body growth, leading to a proportionately smaller FEV₁ and FVC without respiratory impairment, as shown by the normal FEV₁/FVC ratio.

PAI-1 gain-of-function genotype, factors increasing PAI-1 levels, and airway obstruction: The GALA II Cohort

BACKGROUND

PAI-1 gain-of-function variants promote airway fibrosis and are associated with asthma and with worse lung function in subjects with asthma.

OBJECTIVE

We sought to determine whether the association of a gain-of-function polymorphism in plasminogen activator inhibitor-1 (PAI-1) with airway obstruction is modified by asthma status, and whether any genotype effect persists after accounting for common exposures that increase PAI-1 level.

METHODS

We studied 2070 Latino children (8-21y) with genotypic and pulmonary function data from the GALA II cohort. We estimated the relationship of the PAI-1 risk allele with FEV1/FVC by multivariate linear regression, stratified by asthma status. We examined the association of the polymorphism with asthma and airway obstruction within asthmatics via multivariate logistic regression. We replicated associations in the SAPPHIRE cohort of African Americans (n=1056). Secondary analysis included the effect of the at-risk polymorphism on postbronchodilator lung function.

RESULTS

There was an interaction between asthma status and the PAI-1 polymorphism on FEV₁ /FVC (P=.03). The gain-of-function variants, genotypes (AA/AG), were associated with lower FEV₁ /FVC in subjects with asthma (β=-1.25, CI: -2.14,-0.35, P=.006), but not in controls. Subjects with asthma and the AA/AG genotypes had a 5% decrease in FEV₁ /FVC (P<.001). In asthmatics, the risk genotype (AA/AG) was associated with a 39% increase in risk of clinically relevant airway obstruction (OR=1.39, CI: 1.01, 1.92, P=.04). These associations persisted after exclusion of factors that increase PAI-1 including tobacco exposure and obesity.

CONCLUSIONS AND CLINICAL RELEVANCE

The decrease in the FEV₁ /FVC ratio associated with the risk genotype was modified by asthma status. The genotype increased the odds of airway obstruction by 75% within asthmatics only. As exposures known to increase PAI-1 levels did not mitigate this association, PAI-1 may contribute to airway obstruction in the context of chronic asthmatic airway inflammation.

Race is associated with differences in airway inflammation in patients with asthma

BACKGROUND

African American subjects have a greater burden from asthma compared with white subjects. Whether the pattern of airway inflammation differs between African American and white subjects is unclear.

OBJECTIVE

We sought to compare sputum airway inflammatory phenotypes of African American and white subjects treated or not with inhaled corticosteroids (ICSs; ICS+ and ICS-, respectively).

METHODS

We performed a secondary analysis of self-identified African American and white subjects with asthma enrolled in clinical trials conducted by the National Heart, Lung, and Blood Institute-sponsored Asthma Clinical Research Network and AsthmaNet. Demographics, clinical characteristics, and sputum cytology after sputum induction were examined. We used a sputum eosinophil 2% cut point to define subjects with either an eosinophilic (≥2%) or noneosinophilic (<2%) inflammatory phenotype.

RESULTS

Among 1018 participants, African American subjects (n = 264) had a lower FEV1 percent predicted (80% vs 85%, P < .01), greater total IgE levels (197 vs 120 IU/mL, P < .01), and a greater proportion with uncontrolled asthma (43% vs 28%, P < .01) compared with white subjects (n = 754). There were 922 subjects in the ICS+ group (248 African American and 674 white subjects) and 298 subjects in the ICS- group (49 African American and 249 white subjects). Eosinophilic airway inflammation was not significantly different between African American and white subjects in either group (percentage with eosinophilic phenotype: ICS+ group: 19% vs 16%, P = .28; ICS- group: 39% vs 35%, P = .65; respectively). However, when adjusted for confounding factors, African American subjects were more likely to exhibit eosinophilic airway inflammation than white subjects in the ICS+ group (odds ratio, 1.58; 95% CI, 1.01-2.48; P = .046) but not in the ICS- group (P = .984).

CONCLUSION

African American subjects exhibit greater eosinophilic airway inflammation, which might explain the greater asthma burden in this population.

Air Pollution and Lung Function in Minority Youth with Asthma in the GALA II (Genes-Environments and Admixture in Latino Americans) and SAGE II (Study of African Americans, Asthma, Genes, and Environments) Studies

RATIONALE

Adverse effects of exposures to ambient air pollution on lung function are well documented, but evidence in racial/ethnic minority children is lacking.

OBJECTIVES

To assess the relationship between air pollution and lung function in minority children with asthma and possible modification by global genetic ancestry.

METHODS

The study population consisted of 1,449 Latino and 519 African American children with asthma from five different geographical regions in the mainland United States and Puerto Rico. We examined five pollutants (particulate matter ≤10 μm and ≤2.5 μm in diameter, ozone, nitrogen dioxide, and sulfur dioxide), derived from participant residential history and ambient air monitoring data, and assessed over several time windows. We fit generalized additive models for associations between pollutant exposures and lung function parameters and tested for interaction terms between exposures and genetic ancestry.

MEASUREMENTS AND MAIN RESULTS

A 5 μg/m(3) increase in average lifetime particulate matter less than or equal to 2.5 μm in diameter exposure was associated with a 7.7% decrease in FEV1 (95% confidence interval = -11.8 to -3.5%) in the overall study population. Global genetic ancestry did not appear to significantly modify these associations, but percent African ancestry was a significant predictor of lung function.

CONCLUSIONS

Early-life particulate exposures were associated with reduced lung function in Latino and African American children with asthma. This is the first study to report an association between exposure to particulates and reduced lung function in minority children in which racial/ethnic status was measured by ancestry-informative markers.

Self-reported racial/ethnic discrimination and bronchodilator response in African American youth with asthma

IMPORTANCE

Asthma is a multifactorial disease composed of endotypes with varying risk profiles and outcomes. African Americans experience a high burden of asthma and of psychosocial stress, including racial discrimination. It is unknown which endotypes of asthma are vulnerable to racial/ethnic discrimination.

OBJECTIVE

We examined the association between self-reported racial/ethnic discrimination and bronchodilator response (BDR) among African American youth with asthma ages 8 to 21 years (n = 576) and whether this association varies with tumor necrosis factor alpha (TNF-α) level.

MATERIALS AND METHODS

Self-reported racial/ethnic discrimination was assessed by a modified Experiences of Discrimination questionnaire as none or any. Using spirometry, BDR was specified as the mean percentage change in forced expiratory volume in one second before and after albuterol administration. TNF-α was specified as high/low levels based on our study population mean. Linear regression was used to examine the association between self-reported racial/ethnic discrimination and BDR adjusted for selected characteristics. An interaction term between TNF-α levels and self-reported racial/ethnic discrimination was tested in the final model.

RESULTS

Almost half of participants (48.8%) reported racial/ethnic discrimination. The mean percent BDR was higher among participants reporting racial/ethnic discrimination than among those who did not (10.8 versus 8.9, p = 0.006). After adjustment, participants reporting racial/ethnic discrimination had a 1.7 (95% CI: 0.36-3.03) higher BDR mean than those not reporting racial/ethnic discrimination. However, we found heterogeneity of this association according to TNF-α levels (p-interaction = 0.040): Among individuals with TNF-α high level only, we observed a 2.78 higher BDR mean among those reporting racial/ethnic discrimination compared with those not reporting racial/ethnic discrimination (95%CI: 0.79-4.77).

CONCLUSIONS

We found BDR to be increased in participants reporting racial/ethnic discrimination and this association was limited to African American youth with TNF-α high asthma, an endotype thought to be resistant to traditional asthma medications. These results support screening for racial/ethnic discrimination in those with asthma as it may reclassify disease pathogenesis.