Miriam Gjerdevik

A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts

Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. Prior samples were also small for investigating effects by cleft type and exclusively studied isolated clefts (those occurring without other birth defects). We estimated the effects of 17 top loci on cleft types in both isolated and nonisolated cases in the largest consortium to date of European-descent population-based studies. Our analytic approach focused on a mother-child dyad case-control design, but it also allowed analyzing mother-only or child-only genotypes to maximize power. Our total sample included 1,875 cases with isolated clefts, 459 cases with nonisolated clefts, and 3,749 controls. After correcting for multiple testing, we observed significant associations between fetal single-nucleotide polymorphisms (SNPs) at IRF6, PAX7, 8q21.3, 8q24, KIAA1598-VAX1, and MAFB and isolated cleft lip only (CLO) and cleft lip and palate (CLP). Significant associations were observed between isolated CLO and fetal SNPs near TPM1 and NOG1 and between CLP and fetal SNPs at ABCA4-ARHGAP29, THADA, FOXE1, and SPRY2. Overall, effects were similar for isolated CLO and CLP, except for ABCA4-ARHGAP29. A protective effect was observed for the fetal NOG1 SNP on cleft palate only, opposite in direction to the effect on CLO. For most fetal SNPs, a dose-response allelic effect was observed. No evidence of parent-of-origin or maternal genome effects was observed. Overall, effect direction and magnitude were similar between isolated and nonisolated clefts, suggesting that several loci are modifiers of cleft risk in both isolated and nonisolated forms. Our results provide reliable estimates of the effects of top loci on risks of oral clefts in a population of European descent.

A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts

Background GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO) and excess of males with cleft lip with or without cleft palate (CL/P). Methods Genotypes for 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European isolated cleft triads were available from a previously published GWAS. The R-package HAPLIN enables genome-wide–level analyses as well as statistical power simulations for a range of biologic scenarios. We analyzed isolated CL/P and isolated CPO for each ethnicity in HAPLIN, using a sliding-window approach to haplotype analysis and two different statistical models, with and without X-inactivation in females. Results There was a larger number of associations in the Asian versus the European sample, and similar to previous reports that have analyzed the same GWAS dataset using different methods, we identified associations with EFNB1/PJA1 and DMD. In addition, new associations were detected with several other genes, among which KLHL4, TBX22, CPXCR1 and BCOR were noteworthy because of their roles in clefting syndromes. A few of the associations were only detected by one particular X-inactivation model, whereas a few others were only detected in one sex. Discussion/Conclusion We found new support for the involvement of X-linked variants in isolated clefts. The associations were specific for ethnicity, sex and model parameterization, highlighting the need for flexible tools that are capable of detecting and estimating such effects. Further efforts are needed to verify and elucidate the potential roles of EFNB1/PJA1, KLHL4, TBX22, CPXCR1 and BCOR in isolated clefts.

Improving the error rates of the Begg and Mazumdar test for publication bias in fixed effects meta-analysis

BackgroundThe rank correlation test introduced by Begg and Mazumdar is extensively used in meta-analysis to test for publication bias in clinical and epidemiological studies. It is based on correlating the standardized treatment effect with the variance of the treatment effect using Kendall’s tau as the measure of association. To our knowledge, the operational characteristics regarding the significance level of the test have not, however, been fully assessed.MethodsWe propose an alternative rank correlation test to improve the error rates of the original Begg and Mazumdar test. This test is based on the simulated distribution of the estimated measure of association, conditional on sampling variances. Furthermore, Spearman’s rho is suggested as an alternative rank correlation coefficient. The attained level and power of the tests are studied by simulations of meta-analyses assuming the fixed effects model.ResultsThe significance levels of the original Begg and Mazumdar test often deviate considerably from the nominal level, the null hypothesis being rejected too infrequently. It is proven mathematically that the assumptions for using the rank correlation test are not strictly satisfied. The pairs of variables fail to be independent, and there is a correlation between the standardized effect sizes and sampling variances under the null hypothesis of no publication bias. In the meta-analysis setting, the adverse consequences of a false negative test are more profound than the disadvantages of a false positive test. Our alternative test improves the error rates in fixed effects meta-analysis. Its significance level equals the nominal value, and the Type II error rate is reduced. In small data sets Spearman’s rho should be preferred to Kendall’s tau as the measure of association.ConclusionsAs the attained significance levels of the test introduced by Begg and Mazumdar often deviate greatly from the nominal level, modified rank correlation tests, improving the error rates, should be preferred when testing for publication bias assuming fixed effects meta-analysis.

Parent-of-origin-environment interactions in case-parent triads with or without independent controls

With case–parent triad data, one can frequently deduce parent of origin of the childs alleles. This allows a parent‐of‐origin (PoO) effect to be estimated as the ratio of relative risks associated with the alleles inherited from the mother and the father, respectively. A possible cause of PoO effects is DNA methylation, leading to genomic imprinting. Because environmental exposures may influence methylation patterns, gene–environment interaction studies should be extended to allow for interactions between PoO effects and environmental exposures (i.e., PoOxE). One should thus search for loci where the environmental exposure modifies the PoO effect.

Genome-wide analysis of parent-of-origin interaction effects with environmental exposure (PoOxE): An application to European and Asian cleft palate trios

Cleft palate only is a common birth defect with high heritability. Only a small fraction of this heritability is explained by the genetic variants identified so far, underscoring the need to investigate other disease mechanisms, such as gene-environment (GxE) interactions and parent-of-origin (PoO) effects. Furthermore, PoO effects may vary across exposure levels (PoOxE effects). Such variation is the focus of this study. We upgraded the R-package Haplin to enable direct tests of PoOxE effects at the genome-wide level. From a previous GWAS, we had genotypes for 550 case-parent trios, of mainly European and Asian ancestry, and data on three maternal exposures (smoking, alcohol, and vitamins). Data were analyzed for Europeans and Asians separately, and also for all ethnicities combined. To account for multiple testing, a false discovery rate method was used, where q-values were generated from the p-values. In the Europeans-only analyses, interactions with maternal smoking yielded the lowest q-values. Two SNPs in the ‘Interactor of little elongation complex ELL subunit 1’ (ICE1) gene had a q-value of 0.14, and five of the 20 most significant SNPs were in the ‘N-acetylated alpha-linked acidic dipeptidase-like 2’ (NAALADL2) gene. No evidence of PoOxE effects was found in the other analyses. The connections to ICE1 and NAALADL2 are novel and warrant further investigation. More generally, the new methodology presented here is easily applicable to other traits and exposures in which a family-based study design has been implemented.

Incidence of non-pulmonary cancer and lung cancer by amount of emphysema and airway wall thickness: a community-based cohort

There is limited knowledge about the prognostic value of quantitative computed tomography (CT) measures of emphysema and airway wall thickness in cancer. The aim of this study was to investigate if using CT to quantitatively assess the amount of emphysema and airway wall thickness independently predicts the subsequent incidence of non-pulmonary cancer and lung cancer. In the GenKOLS study of 2003–2005, 947 ever-smokers performed spirometry and underwent CT examination. The main predictors were the amount of emphysema measured by the percentage of low attenuation areas (%LAA) on CT and standardised measures of airway wall thickness (AWT-PI10). Cancer data from 2003–2013 were obtained from the Norwegian Cancer Register. The hazard ratio associated with emphysema and airway wall thickness was assessed using Cox proportional hazards regression for cancer diagnoses. During 10 years of follow-up, non-pulmonary cancer was diagnosed in 11% of the subjects with LAA <3%, in 19% of subjects with LAA 3–10%, and in 17% of subjects with LAA ≥10%. Corresponding numbers for lung cancer were 2%, 3% and 11%, respectively. After adjustment, the baseline amount of emphysema remained a significant predictor of the incidence of non-pulmonary cancer and lung cancer. Airway wall thickness did not predict cancer independently. This study offers a strong argument that emphysema is an independent risk factor for both non-pulmonary cancer and lung cancer. Emphysema is an independent risk factor for both non-pulmonary cancer and lung cancer http://ow.ly/SPR1308EgYn

Randomised comparison of needle aspiration and chest tube drainage in spontaneous pneumothorax

Guidelines on spontaneous pneumothorax are contradictory as to intervention between needle aspiration (NA) and chest tube drainage (CTD). Studies show poor adherence to guidelines. Three Norwegian hospitals included patients with primary (PSP) and secondary (SSP) spontaneous pneumothorax. Patients underwent NA or CTD as the primary intervention. The main outcome was duration of hospital stay. Secondary outcomes were immediate- and 1-week success rates and complications. 127 patients were included, including 48 patients with SSP. 65 patients underwent NA, 63 patients CTD. Median (interquartile range) hospital stay was significantly shorter for NA: 2.4 days (1.2–4.7 days), compared with CTD: 4.6 days (2.3–7.8 days) (p<0.001). The corresponding figures for the SSP subgroup were 2.54 days (1.17–7.79 days) compared with 5.53 days (3.65–9.21 days) (p=0.049) for NA and CTD, respectively. Immediate success rates were 69% for NA compared with 32% for CTD (p<0.001). The positive effect of NA remained significant in sub-analyses for SSP. There was no significant difference in 1-week success rates. Complications occurred only during the CTD-treatment. Our study shows shorter hospital stay and higher immediate success rates for NA compared with CTD. Subgroup analyses also show clear benefits for NA for both PSP and SSP. Needle aspiration as treatment leads to shorter hospital stay in primary and secondary spontaneous pneumothorax http://ow.ly/tmMU309dB8V

Pneumothorax size measurements on digital chest radiographs: Intra- and inter- rater reliability

PURPOSE Detailed and reliable methods may be important for discussions on the importance of pneumothorax size in clinical decision-making. Rheas method is widely used to estimate pneumothorax size in percent based on chest X-rays (CXRs) from three measure points. Chois addendum is used for anterioposterior projections. The aim of this study was to examine the intrarater and interrater reliability of the Rhea and Choi method using digital CXR in the ward based PACS monitors. MATERIALS AND METHODS Three physicians examined a retrospective series of 80 digital CXRs showing pneumothorax, using Rhea and Chois method, then repeated in a random order two weeks later. We used the analysis of variance technique by Eliasziw et al. to assess the intrarater and interrater reliability in altogether 480 estimations of pneumothorax size. RESULTS Estimated pneumothorax sizes ranged between 5% and 100%. The intrarater reliability coefficient was 0.98 (95% one-sided lower-limit confidence interval C 0.96), and the interrater reliability coefficient was 0.95 (95% one-sided lower-limit confidence interval 0.93). CONCLUSION This study has shown that the Rhea and Choi method for calculating pneumothorax size has high intrarater and interrater reliability. These results are valid across gender, side of pneumothorax and whether the patient is diagnosed with primary or secondary pneumothorax.

The Relationship of Educational Attainment with Pulmonary Emphysema and Airway Wall Thickness

RATIONALE Low educational attainment is a risk factor of chronic obstructive pulmonary disease (COPD). There is limited knowledge on the relationship between educational level and computed tomography measures of emphysema and airway wall thickness (AWT). OBJECTIVES We hypothesized that low educational attainment is associated with increased emphysema and AWT in ever-smokers with and without COPD. METHODS We included 462 and 485 ever-smokers with and without COPD in a cross-sectional study, aged 40-86 years. The sample was divided into groups reflecting educational attainment: primary, secondary, and university. We performed linear regression to examine associations between educational attainment and both emphysema and AWT separately for those with and without COPD. We adjusted for sex, age, smoking status, age of onset of smoking, pack-years, height, and body mass index. MEASUREMENTS AND MAIN RESULTS Compared with university education, in subjects with COPD, primary education was associated with a 68.1% (95% confidence interval = 14.2-147.6%; P = 0.01) relative increase in emphysema and secondary education was associated with a 50.6% (95% confidence interval = 5.7-114.6%; P = 0.02) relative increase. There was a nonsignificant trend toward an association between lower educational attainment and increased emphysema among those without COPD (P = 0.18), yet greater age appeared to modify this association (P = 0.01). We did not detect significant linear relationships between educational attainment and AWT in subjects with or without COPD. CONCLUSIONS Lower educational attainment was associated with increased emphysema among adults with COPD. Among those without COPD, this association was more pronounced with increasing age. No significant linear relationship between educational attainment and AWT was found. Clinicians treating adults with emphysema should keep in mind that factors related to low education beyond that of smoking and occupational dust exposure might be of importance to the disease.

A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG

Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry. A GxE effect is present if the relative risk estimates for gene-effects in the offspring are different across exposure strata. We tested this using the relative risk ratio (RRR). Besides analyzing all ethnicities combined (“pooled analysis”), separate analyses were conducted on Europeans and Asians to investigate ethnicity-specific effects. To control for multiple testing, q-values were calculated from the p-values. Results: We identified significant GxVitamin interactions with three SNPs in “Estrogen-related receptor gamma” (ESRRG) in the pooled analysis. The RRRs (95% confidence intervals) were 0.56 (0.45–0.69) with rs1339221 (q = 0.011), 0.57 (0.46–0.70) with rs11117745 (q = 0.011), and 0.62 (0.50–0.76) with rs2099557 (q = 0.037). The associations were stronger when these SNPs were analyzed as haplotypes composed of two-SNP and three-SNP combinations. The strongest effect was with the “t-t-t” haplotype of the rs1339221-rs11117745-rs2099557 combination [RRR = 0.50 (0.40–0.64)], suggesting that the effects observed with the other SNP combinations, including those in the single-SNP analyses, were mainly driven by this haplotype. Although there were potential GxVitamin effects with rs17734557 and rs1316471 and GxAlcohol effects with rs9653456 and rs921876 in the European sample, respectively, none of the SNPs was located in or near genes with strong links to orofacial clefts. GxAlcohol and GxSmoke effects were not assessed in the Asian sample because of a lack of observations for these exposures. Discussion/Conclusion: We identified significant interactions between vitamin use and variants in ESRRG in the pooled analysis. These GxE effects are novel and warrant further investigations to elucidate their roles in orofacial clefting. If validated, they could provide prospects for exploring the impact of estrogens and vitamins on clefting, with potential translational applications.