Purpose:This study evaluated the long-term safety of roflumilast in patients with chronic obstructive pulmonary disease or chronic bronchitis using electronic healthcare databases from Germany, Norway, Sweden, and the United States (US). Patients and Methods:The study population consisted of patients aged ≥40 years who had been exposed to roflumilast and a matched cohort unexposed to roflumilast. The matching was based on sex, age, calendar year of cohort entry date (2010-2011, 2012, or 2013), and a propensity score that included variables such as demographics, markers of chronic obstructive pulmonary disease (COPD) severity and morbidity, and comorbidities. In comparison to the unexposed matched cohort (never use), three exposure definitions were used for the exposed matched cohort: ever use, use status (current, recent, past use), and cumulative duration of use. The main outcome was 5-year all-cause mortality. Cox regression models were used to estimate crude and adjusted hazard ratios (HRs) and 95% confidence intervals (CI). Results:112,541 unexposed and 23,239 exposed patients across countries were included. Some variables remained unbalanced after matching, indicating higher COPD disease severity among the exposed patients. Adjusted HRs of 5-year all-cause mortality for "ever use" of roflumilast, compared to "never use", were 1.12 (95% CI, 1.08-1.17) in Germany, 1.00 (95% CI, 0.92-1.08) in Norway, 0.98 (95% CI, 0.92-1.04) in Sweden, and 1.16 (95% CI, 1.12-1.20) in the US. Compared to never users, there was a decrease in 5-year mortality risk observed among "current users" in Germany (HR: 0.93, 95% CI: 0.88-0.98), Norway (HR: 0.77, 95% CI: 0.67-0.87), and Sweden (HR: 0.80, 95% CI: 0.73-0.88). Conclusion:There was no observed increase in 5-year mortality risk with the use of roflumilast in Sweden or Norway. A small increase in 5-year mortality risk was observed in Germany and the US in the ever versus never comparison, likely due to residual confounding by indication.

To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin. We identified five histotype-specific EOC risk regions (p value <5 × 10-8) and confirmed previously reported associations for 27 risk regions. Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (p value <10-5). Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype. Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue datasets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (false discovery rate <0.05). Finally, by integrating genome-wide HiChIP interactome analysis with transcriptome-wide association study (TWAS), variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8, and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by a genome-wide association study.

Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, “select and shrink for summary statistics” (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28–1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08–1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21–1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29–1.43, AUC: 0.592) in BRCA1 pathogenic variant carriers and 1.49 (95% CI: 1.35–1.64, AUC: 0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.

Candidate causal risk variants from genome-wide association studies reside almost exclusively in noncoding regions of the genome and innovative approaches are necessary to understand their biological function. Multi-marker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA to create chromatin-MAGMA (chromMAGMA), a method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants for complex diseases.

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03286-9.

Quantifying the functional effects of complex disease risk variants can provide insights into mechanisms underlying disease biology. Genome wide association studies (GWAS) have identified 39 regions associated with risk of epithelial ovarian cancer (EOC). The vast majority of these variants lie in the non-coding genome, suggesting they mediate their function through the regulation of gene expression by their interaction with tissue specific regulatory elements (REs). In this study, by intersecting germline genetic risk data with regulatory landscapes of active chromatin in ovarian cancers and their precursor cell types, we first estimated the heritability explained by known common low penetrance risk alleles. The narrow sense heritability of both EOC overall and high grade serous ovarian cancer (HGSOCs) was estimated to be 5-6%. Partitioned SNP-heritability across broad functional categories indicated a significant contribution of regulatory elements to EOC heritability. We collated epigenomic profiling data for 77 cell and tissue types from public resources (Roadmap Epigenomics and ENCODE), and H3K27Ac ChIP-Seq data generated in 26 ovarian cancer-relevant cell types. We identified significant enrichment of risk SNPs in active REs marked by H3K27Ac in HGSOCs. To further investigate how risk SNPs in active REs influence predisposition to ovarian cancer, we used motifbreakR to predict the disruption of transcription factor binding sites. We identified 469 candidate causal risk variants in H3K27Ac peaks that break TF motifs (enrichment P-Value < 1×10 −5 compared to control variants). The most frequently broken motif was REST (P-Value = 0.0028), which has been reported as both a tumor suppressor and an oncogene. These systematic functional annotations with epigenomic data highlight the specificity of the regulatory landscape and demonstrate functional annotation of germline risk variants is most informative when performed in highly relevant cell types.

The vaginal microbiota is thought to play a role in modulating risk of high-risk human papillomavirus (hrHPV) infection. We examined the relationship between the vaginal microbiota and persistent hrHPV infection in HIV-negative and HIV-positive women. We used 16S-rRNA sequencing to characterize the vaginal microbiota of two serial samples taken six months apart from 211 Nigerian women (67%, 142/211 HIV-positive and 33%, 69/211 HIV-negative) and evaluated the association between the vaginal microbiota and persistent hrHPV infection using generalized estimating equation logistic regression models and linear discriminant analysis effect size (LEfSe) algorithm to identify phylotypic biomarkers of persistent hrHPV infection. The high diversity microbiota, Community State Type IV-B, was the most prevalent in both HIV-negative (38% at baseline, 30% at the follow-up visit) and HIV-positive (27% at baseline, 35% at the follow-up visit) women. The relationship between the vaginal microbiota and persistent hrHPV was modified by HIV status. In HIV-negative women, women with Lactobacillus dominant microbiota had lower odds (OR: 0.35, 95% CI 0.14–0.89, p = 0.03) of persistent hrHPV compared to women with Lactobacillus deficient microbiota. While among HIV-positive women, the odds of being persistently infected with hrHPV was higher in women with Lactobacillus dominant microbiota (OR: 1.25, 95% CI 0.73–2.14 p = 0.41). This difference in effect estimates by HIV was statistically significant (p = 0.02). A high diversity vaginal microbial community with paucity of Lactobacillus species was associated with persistent hrHPV infection in HIV-negative women but not in HIV-positive women.

Genital warts are important causes of morbidity and their prevalence and incidence can be used to evaluate the impact of HPV vaccination in a population.

Background: Reports from previous studies suggest that the vaginal microbiota may play a role in cervical HPV pathogenesis. In this study, we examined associations between the vaginal microbiome and persistent high-risk human papillomarvirus (hrHPV) infection among HIV-negative and HIV-positive women. Methods: We used 16S rRNA gene amplicon sequencing to characterize the vaginal microbiota in 2 serial mid-vaginal samples taken approximately 6 months apart in 211 Nigerian women and the SPF 10 LIPA 25 system for HPV detection. We used generalized estimating equation (GEE) logistic regression models with robust variance estimation and the cluster option for repeated measures, to evaluate the association between the vaginal microbiota composition and persistent hrHPV infection (defined as being positive for hrHPV at 2 visits 6 months apart); Linear discriminant analysis effect size (LEfSe) to identify phylotype biomarkers of persistent hrHPV; Markov chain transition probabilities to evaluate transition patterns and hierarchical clustering algorithms for community state (CST) assignments. Results: Some 142 women were HIV-positive and 69 were HIV-negative. Of the 211 participants, 71 were persistently positive for hrHPV. Mean age (SD) of participants was 38 (8) years. Most participants (84%, 175/211) were premenopausal. High diversity, low Lactobacillus spp. bacterial community state types, CST IV (A and B) were the most prevalent community state types (CST) in HIV-negative (57% at baseline and 40% at the follow-up visit) and HIV-positive (73% at baseline and 65% at the follow-up visit) women. There was effect modification by HIV status ( P = 0.02). Among HIV-negative women, those who had a high relative abundance of Lactobacillus spp. were less likely to have persistent hrHPV (OR: 0.35, 95% CI: 0.14 to 0.89, P = 0.03) compared to women with low relative abundance of Lactobacillus spp. LEfSe analysis identified Sneathia spp as being differentially more abundant in HIV-negative women with persistent hrHPV. Markov chain transition probabilities showed that most CST transitions were to the highly diverse, low Lactobacillus spp., CST IV. In HIV-positive women, there was no significant association between the relative abundance of Lactobacillus spp and persistent hrHPV. Conclusions: Our results provide evidence to suggest that persistent hrHPV is associated with a lack of Lactobacillus spp in the vaginal microbiota of HIV-negative women.

Background: There is exponential growth in the interest and implementation of genomics research in Africa. This growth has been facilitated by the Human Hereditary and Health in Africa (H3Africa) initiative, which aims to promote a contemporary research approach to the study of genomics and environmental determinants of common diseases in African populations.Objective: The purpose of this article is to describe important challenges affecting genomics research implementation in Africa.Methods: The observations, challenges and recommendations presented in this article were obtained through discussions by African scientists at teleconferences and face-to-face meetings, seminars at consortium conferences and in-depth individual discussions.Results: Challenges affecting genomics research implementation in Africa, which are related to limited resources include ill-equipped facilities, poor accessibility to research centers, lack of expertise and an enabling environment for research activities in local hospitals. Challenges related to the research study include delayed funding, extensive procedures and interventions requiring multiple visits, delays setting up research teams and insufficient staff training, language barriers and an underappreciation of cultural norms. While many African countries are struggling to initiate genomics projects, others have set up genomics research facilities that meet international standards.Conclusions: The lessons learned in implementing successful genomics projects in Africa are recommended as strategies to overcome these challenges. These recommendations may guide the development and application of new research programs in low-resource settings.

Purpose There is a dearth of data on clearance of cervical human papillomavirus (HPV) infection among women in West Africa. We examined the clearance of low-risk (lr) and high-risk (hr) cervical HPV infections, and the factors associated with these measures in HIV-negative and HIV-positive women. Methods We studied 630 Nigerian women involved in a study of HPV infection using short polymerase chain reaction fragment-10 assay and line probe assay-25. Research nurses used a cervical brush to collect samples of exfoliated cervical cells from all the study participants. Cox proportional hazards models were used to estimate associations between HIV and HPV infections. Results The mean age of the study participants was 38 (standard deviation, ± 8) years; 51% were HIV positive. The rate of clearing any HPV infection was 2.0% per month among all women in the study population, 2.5% per month among HIV-negative women, and 1.6% per month, among HIV-positive women. The clearance rate per 1,000 person-months of observation for any lrHPV infection and any hrHPV infection were 9.21 and 8.83, respectively, for HIV-negative women, and 9.38 and 9.37, respectively, for HIV-positive women. In multivariate models, the hazard ratios for HIV-positive compared with HIV-negative women were 0.85 (95% CI, 0.51 to 1.43; P = .55) and 0.95 (95% CI, 0.54 to 1.65; P = .85) for cleared infections with any lrHPV and any hrHPV, respectively. The hazard ratio for HIV-positive compared with HIV-negative women was 0.39 (95% CI, 0.17 to 0.88; P = .02) for cleared infections with any multiple HPV and 0.13 (95% CI, 0.03 to 0.58; P = .007) for cleared infections with multiple hrHPV. Conclusion In this study population, we observed that HIV-positive women were less likely to clear infections with multiple hrHPV types.

ObjectiveIn low resource settings, visual inspection with acetic acid (VIA) by allied health workers, has been suggested as an alternative for cervical cancer screening. However, there are concerns about the objectivity and time to diagnostic concordance with specialists. We evaluated the secular trend in interobserver agreement between nurse providers and a gynecologist/colposcopist over a five-year period.MethodsNurses provided VIA screening with digital cervivography to 4,961 participants in five screening clinics from October 2010 to May 2014 in Nigeria in this observational study. Cervigraphs were reviewed at meetings where a gynaecologist/colposcopist made an assessment from the cervigraphs. We used weighted kappa statistics to calculate agreement in diagnosis between nurse providers and the gynecologist/colposcopist; linear regression models to examine overall trend and investigate potential clinic characteristics that may influence agreement; and time series models to characterize month to month variations.ResultsMean age of participants was 37±8 years. Overall agreement was 0.89 at Site D, 0.78 and 0.73 at Sites A and C respectively, 0.50 for Site E and 0.34 for Site C. The number of trainings attended by nurse providers(β = 0.47,95%CI:0.02-0.93, p = 0.04), high level of engagement by site gynecologists(β = 0.11,95%CI:0.01-0.21,p = 0.04) were associated with increased agreement; while increasing distance from the coordinating site(β = -0.47,95%CI:-0.92-0.02,p = 0.04) was associated with decreased agreement. There were no associations between number of years screening clinics were operational(β = 0.01,95%CI: -0.01-0.03,p = 0.29), cumulative experience of nurse providers(β = 0.04,95%CI:-0.03-0.12,p = 0.19) and agreement. There were no significant increases in weighted kappa statistics over time for all sites considered. Monthly variations were significant for only one of two sites considered in time series models (AR1 term = -0.40, 95%CI:-0.71-0.09,p = 0.01).ConclusionOur results showed a lack of objectivity, persistent variation and lack of convergence of diagnostic capabilities of nurse led VIA cervical cancer screening with the diagnostic capabilities of a specialist in a cervical cancer screening program in Nigeria.

OBJECTIVES:We explored determinants of attrition in a longitudinal cohort study in Nigeria. STUDY DESIGN AND SETTING:We enrolled 1,020 women into a prospective study. Of these, 973 were eligible to return for follow-up. We investigated the determinants of attrition among eligible women using a sequential mixed methods design. We used logistic regression models to compare the baseline characteristics of responders and nonresponders. At the end of the parent study, we conducted four focus group discussions and eight key informant interviews with nonresponders. RESULTS:Of the 973 women included in the quantitative analysis, 26% were nonresponders. From quantitative analysis, older women were less likely to drop out than younger women (reference: women ≤30 years; OR 0.46; 95% confidence interval [CI] 0.30-0.70, P < 0.001 women 31-44 years; and OR 0.31; 95% CI 0.17-0.56, P < 0.001 women ≥45 years). HIV-positive women were also less likely to drop out of the study (OR 0.45; 95% CI 0.33-0.63, P < 0.001). From qualitative analysis, contextual factors that influenced attrition were high cost of participation, therapeutic misconceptions, inaccurate expectations, spousal disapproval, unpleasant side effects, challenges in maintaining contact with participants, and participant difficulties in locating the study clinic. CONCLUSION:Several participant-, research-, and environment-related factors influence attrition. Retention strategies that address these barriers are important to minimize attrition.

1510 Background: Cervical cancer is the second commonest cancer in Africa. Persistent High-risk HPV (HRHPV) infection is a necessary cause but little is known about the persistence and associated risk factors of HRHPV infection in African women. The aim of this study was to determine risk factors and incidence of HPV infection in Nigerian women. Methods: ACCME is a multicenter prospective cohort study of host germline, cervical somatic and HRHPV genomics, epigenomics, and vaginal microenvironment; and their association with HPV. From February/2014 to January/2016, 10,000 HIV-negative women were enrolled into the cohort and are being followed up every 6 months. We used SPF 25 /LiPA 10 to characterize HPV infection and defined persistent infection as 2 consecutive positive tests done at least 12 months apart. Logistic regression models were used to estimate the associations between risk factors and persistent HPV. Results: The mean (SD) age of the study participants at baseline was 40 (10) years and the mean (SD) vaginal pH was 5.2 (0.6). About 42% of the participants were positive for any HPV positive and 21% had persistence of any HPV infections. Some, 35% of the participants had multiple infections with any HPV. About 54% of those with persistent any HPV infections had HRHPV; HPV types 52 (25%) and 18 (15%) were the most prevalent and persistent HRHPV types. The incidence of any HPV infection was 6.6/1,000 person-months while that of HRHPV was 2.6/1,000 person-months. Age, body mass index, level of education, marital and socio-economic status and total number of lifetime sexual partners were associated with HPV infection in these women. Conclusions: We defined the incidence, risk factors and commonest types of HRHPV in a large cohort of women in West Africa.

Background: Studies assessing risk of sexual behavior and disease are often plagued by questions about the reliability of self-reported sexual behavior. In this study, we evaluated the reliability of self-reported sexual history among urbanized women in a prospective study of cervical HPV infections in Nigeria.Methods: We examined test-retest reliability of sexual practices using questionnaires administered at study entry and at follow-up visits. We used the root mean squared approach to calculate within-person coefficient of variation (CVw) and calculated the intra-class correlation coefficient (ICC) using two way, mixed effects models for continuous variables and ((kappa) over cap statistics for discrete variables. To evaluate the potential predictors of reliability, we used linear regression and log binomial regression models for the continuous and categorical variables, respectively.Results: We found that self-reported sexual history was generally reliable, with overall ICC ranging from 0.7 to 0.9; however, the reliability varied by nature of sexual behavior evaluated. Frequency reports of non-vaginal sex (agreement = 63.9%, 95% CI: 47.5-77.6%) were more reliable than those of vaginal sex (agreement = 59.1%, 95% CI: 55.2-62.8%). Reports of time-invariant behaviors were also more reliable than frequency reports. The CVw for age at sexual debut was 10.7 (95% CI: 10.6-10.7) compared with the CVw for lifetime number of vaginal sex partners, which was 35.2 (95% CI: 35.1-35.3). The test-retest interval was an important predictor of reliability of responses, with longer intervals resulting in increased inconsistency (average change in unreliability for each 1 month increase = 0.04, 95% CI = 0.07-0.38, p = 0.005).Conclusion: Our findings suggest that overall, the self-reported sexual history among urbanized Nigeran women is reliable.

Background The prevalence, persistence, and multiplicity of human papillomavirus (HPV) infection appears different comparing HIV-positive to HIV-negative women. In this study, we examined prevalent, persistent, and multiple low- and high-risk cervical HPV infections in HIV-negative and HIV-positive women. Methods We studied 1,020 women involved in a study of HPV infection using SPF25/LiPA10. Two study visits were scheduled, at enrollment and 6 months afterward. At each study visit, research nurses used a cervical brush to collect samples of exfoliated cervical cells from the cervical os, from all the study participants. Exact logistic regression models were used to estimate associations between HIV and HPV infections. Results The mean (SD) age of the study participants was 38 (8) years, 56% were HIV-negative and 44% were HIV-positive. Among HIV-negative women at baseline, single low-risk HPV (lrHPV) infections occurred in 12%; multiple lrHPV in 2%; single high-risk human papillomavirus (hrHPV) infections in 9%, and multiple hrHPV infections in 2%. Single lrHPV infections were persistent in 6%, but there was no persistent multiple lrHPV infections. Single hrHPV infections were persistent in 4% while multiple hrHPV infections were persistent in 0.3%. Among HIV-positive women at baseline, single lrHPV infections occurred in 19%, multiple lrHPV in 6%, single hrHPV infections in 17%, and multiple hrHPV infections occurred in 12%. Single lrHPV infections were persistent in 9%, multiple lrHPV infections in 0.6%, single hrHPV infections in 13%, while multiple hrHPV were persistent in 3%. Prevalent, persistent, and multiple infections were more common in HIV-positive women, compared to HIV-negative women. In multivariate models adjusted for age, marital status, socioeconomic status, age at sexual initiation, and douching, the odds ratios comparing HIV-positive to HIV-negative women, were 2.09 (95% CI 1.47–2.97, p < 0.001) for prevalent lrHPV, 1.26 (95% CI 0.66–2.40, p 0.47) for persistent lrHPV infections, 3.38 (95% CI 2.34–4.87, p < 0.001) for prevalent hrHPV, and 4.49 (95% CI 2.26–8.91, p < 0.001) for persistent hrHPV infections. Conclusion HIV infection was associated with higher prevalence of lrHPV, hrHPV, and persistence hrHPV infections, but not persistent lrHPV infections.

IntroductionAlcohol consumption has been identified as a risk factor for many cancers but less attention has been paid to the fraction of those cancers that are attributable to alcohol consumption. In this study, we evaluated the incidence and population attributable fraction (PAF) of cancers associated with alcohol consumption in Nigeria.MethodsWe obtained data on incidence of cancers from two population-based cancer registries (PBCRs) in Nigeria and identified cancer sites for which there is strong evidence of an association with alcohol consumption based on the International Agency for Research on Cancer Monograph 100E. We computed the PAF for each cancer site by age and sex, using prevalence and relative risk estimates from previous studies.ResultsBetween 2012 and 2014 study period, the PBCRs reported 4,336 cancer cases of which 1,627 occurred in males, and 2,709 occurred in females. Of these, a total of 1,808 cancer cases, 339 in males and 1,469 in females, were associated with alcohol intake. The age standardized incidence rate (ASR) of alcohol associated cancers was 77.3 per 100,000. Only 4.3% (186/4,336) of all cancer cases or 10.3% (186/1,808) of alcohol associated cancers were attributable to alcohol consumption. Some 42.5% (79/186) of these cancers occurred in males while 57.5% (107/186) occurred in females. The ASR of cancers attributable to alcohol in this population was 7.2 per 100,000. The commonest cancers attributable to alcohol consumption were cancers of the oral cavity and pharynx in men and cancer of the breast in women.ConclusionOur study shows that 4.3% of incident cancers in Nigeria can be prevented by avoiding alcohol consumption. While the incidence of cancers associated with alcohol intake is high, the proportion attributable to alcohol consumption is much lower suggesting that the number of cancers that may be prevented by eliminating alcohol intake in this population is relatively low.