Administrative Data Linkage in Brazil: Potentials for Health Technology Assessment

Health technology assessment (HTA) is the systematic evaluation of the properties and impacts of health technologies and interventions. In this article, we presented a discussion of HTA and its evolution in Brazil, as well as a description of secondary data sources available in Brazil with potential applications to generate evidence for HTA and policy decisions. Furthermore, we highlighted record linkage, ongoing record linkage initiatives in Brazil, and the main linkage tools developed and/or used in Brazilian data. Finally, we discussed the challenges and opportunities of using secondary data for research in the Brazilian context. In conclusion, we emphasized the availability of high quality data and an open, modern attitude toward the use of data for research and policy. This is supported by a rigorous but enabling legal framework that will allow the conduct of large-scale observational studies to evaluate clinical, economical, and social impacts of health technologies and social policies.

Propensity Score Methods in Health Technology Assessment: Principles, Extended Applications, and Recent Advances

Randomized clinical trials (RCT) are accepted as the gold-standard approaches to measure effects of intervention or treatment on outcomes. They are also the designs of choice for health technology assessment (HTA). Randomization ensures comparability, in both measured and unmeasured pretreatment characteristics, of individuals assigned to treatment and control or comparator. However, even adequately powered RCTs are not always feasible for several reasons such as cost, time, practical and ethical constraints, and limited generalizability. RCTs rely on data collected on selected, homogeneous population under highly controlled conditions; hence, they provide evidence on efficacy of interventions rather than on effectiveness. Alternatively, observational studies can provide evidence on the relative effectiveness or safety of a health technology compared to one or more alternatives when provided under the setting of routine health care practice. In observational studies, however, treatment assignment is a non-random process based on an individual’s baseline characteristics; hence, treatment groups may not be comparable in their pretreatment characteristics. As a result, direct comparison of outcomes between treatment groups might lead to biased estimate of the treatment effect. Propensity score approaches have been used to achieve balance or comparability of treatment groups in terms of their measured pretreatment covariates thereby controlling for confounding bias in estimating treatment effects. Despite the popularity of propensity scores methods and recent important methodological advances, misunderstandings on their applications and limitations are all too common. In this article, we present a review of the propensity scores methods, extended applications, recent advances, and their strengths and limitations.

Family health and conditional cash transfer in Brazil and its effect on tuberculosis mortality

BACKGROUND

Social protection can reduce poverty and act on the determinants of tuberculosis (TB).

OBJECTIVE

To evaluate the impact of the Family Health Strategy (FHS) and the Bolsa Família Programme on TB-related mortality in Brazil.

METHODS

This was an ecological study in which the units of analysis were Brazilian municipalities between 2001 and 2012. The principal independent variables were the levels of coverage of the primary health care system and the conditional cash transfer programme. The dependent variable was TB mortality rate (obtained from national databases). Descriptive analysis and negative binomial regression based on panel data using fixed-effects models were performed. Crude and adjusted estimates were calculated for continuous and categorical variables.

RESULTS

A high FHS coverage was significantly associated with a reduction in the TB mortality rate (RR 0.80, 95%CI 0.72-0.89). An increase in the coverage of the Brazilian cash transfer programme was significantly associated with a reduction in the TB mortality rate (RR 0.87, 95%CI 0.81-0.96).

CONCLUSION

FHS and the Bolsa Família conditional cash transfer programme had a positive impact on the TB mortality rate in Brazil. Public policies should include economic support combined with health promotion.

Brickley E, C. Rodrigues L, Smeeth L, L. Barreto M, Martins Pereira S, Oliveira Penna G. Geographic and socioeconomic factors associated with leprosy treatment default: An analysis from the 100 Million Brazilian Cohort

BACKGROUND

Although leprosy is largely curable with multidrug therapy, incomplete treatment limits therapeutic effectiveness and is an important obstacle to disease control. To inform efforts to improve treatment completion rates, we aimed to identify the geographic and socioeconomic factors associated with leprosy treatment default in Brazil.

METHODOLOGY/PRINCIPAL FINDINGS

Using individual participant data collected in the Brazilian national registries for social programs and notifiable diseases and linked as part of the 100 Million Brazilian Cohort, we evaluated the odds of treatment default among 20,063 leprosy cases diagnosed and followed up between 2007 and 2014. We investigated geographic and socioeconomic risk factors using a multivariate hierarchical analysis and carried out additional stratified analyses by leprosy subtype and geographic region. Over the duration of follow-up, 1,011 (5.0%) leprosy cases were observed to default from treatment. Treatment default was markedly increased among leprosy cases residing in the North (OR = 1.57; 95%CI 1.25-1.97) and Northeast (OR = 1.44; 95%CI 1.17-1.78) regions of Brazil. The odds of default were also higher among cases with black ethnicity (OR = 1.29; 95%CI 1.01-1.69), no income (OR = 1.41; 95%CI 1.07-1.86), familial income ≤ 0.25 times Brazilian minimum wage (OR = 1.42; 95%CI 1.13-1.77), informal home lighting/no electricity supply (OR = 1.53; 95%CI 1.28-1.82), and household density of > 1 individual per room (OR = 1.35; 95%CI 1.10-1.66).

CONCLUSIONS

The findings of the study indicate that the frequency of leprosy treatment default varies regionally in Brazil and provide new evidence that adverse socioeconomic conditions may represent important barriers to leprosy treatment completion. These findings suggest that interventions to address socioeconomic deprivation, along with continued efforts to improve access to care, have the potential to improve leprosy treatment outcomes and disease control.

Socioeconomic determinants of leprosy new case detection in the 100 Million Brazilian Cohort: a population-based linkage study

BACKGROUND

Although leprosy is recognised as a disease of poverty, there is little evidence on the specific socioeconomic factors associated with disease risk. To inform targeted strategies for disease elimination, we investigated socioeconomic markers of leprosy risk in Brazil.

METHODS

Socioeconomic data from the 100 Million Brazilian Cohort were linked to the Brazilian national disease registry (Sistema de Informação de Agravos de Notificação) for leprosy from Jan 1, 2007, to Dec 31, 2014. Using Poisson regression, we assessed the association of socioeconomic factors with risk of incident leprosy in the full cohort and in children (aged 0-15 years), by leprosy subtype and region of residence.

FINDINGS

In an analysis of 23 899 942 individuals including 18 518 patients with leprosy, increased levels of deprivation were associated with an increased risk of leprosy in Brazil. Directions of effect were consistent in children younger than 15 years and across disease subtypes. Individuals residing in regions with the highest poverty in the country (central-west, north, and northeast regions) had a risk of leprosy incidence five-to-eight times greater than did other individuals. Decreased levels of income and education and factors reflecting unfavourable living conditions were associated with an up to two-times increase in leprosy incidence (incidence rate ratio 1·46, 95% CI 1·32-1·62, for lowest vs highest quartile of income per capita; 2·09, 95% CI 1·62-2·72, for lowest vs highest level of education).

INTERPRETATION

Within the poorest half of the Brazilian population, the most deprived individuals have the greatest risk of leprosy. Strategies focusing on early detection and treatment in the poorest populations could contribute substantially to global disease control.

FUNDING

Medical Research Council, Wellcome Trust, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazil), the Conselho Nacional das Fundações Estaduais de Amparo à Pesquisa, Economic and Social Research Council, Biotechnology and Biological Sciences Research Council, Conselho Nacional de Desenvolvimento Científico e Tecnológico, and Fundação de Apoio à Pesquisa do Distrito Federal.

Dengue during pregnancy and live birth outcomes: a cohort of linked data from Brazil

OBJECTIVES

Dengue is the most common viral mosquito-borne disease, and women of reproductive age who live in or travel to endemic areas are at risk. Little is known about the effects of dengue during pregnancy on birth outcomes. The objective of this study is to examine the effect of maternal dengue severity on live birth outcomes.

DESIGN AND SETTING

We conducted a population-based cohort study using routinely collected Brazilian data from 2006 to 2012.

PARTICIPATING

We linked birth registration records and dengue registration records to identify women with and without dengue during pregnancy. Using multinomial logistic regression and Firth method, we estimated risk and ORs for preterm birth (<37 weeks' gestation), low birth weight (<2500 g) and small for gestational age (<10thcentile). We also investigated the effect of time between the onset of the disease and each outcome.

RESULTS

We included 16 738 000 live births. Dengue haemorrhagic fever was associated with preterm birth (OR=2.4; 95% CI 1.3 to 4.4) and low birth weight (OR=2.1; 95% CI 1.1 to 4.0), but there was no evidence of effect for small for gestational age (OR=2.1; 95% CI 0.4 to 12.2). The magnitude of the effects was higher in the acute disease period.

CONCLUSION

This study showed an increased risk of adverse birth outcomes in women with severe dengue during pregnancy. Medical intervention to mitigate maternal risk during severe acute dengue episodes may improve outcomes for infants born to exposed mothers.

Environmental Risks of Cities in the European Region: Analyses of the Sustainable Healthy Urban Environments (SHUE) Database

INTRODUCTION

In an increasingly urbanized world, cities are a key focus for action on health and sustainability. The Sustainable Healthy Urban Environments (SHUE) project aims to provide a shared information resource to support such action. Its aim is to test the feasibility and methods of assembling data about the characteristics of a globally distributed sample of cities and the populations within them for comparative analyses, and to use such data to assess how policies may contribute to sustainable urban development and human health.

METHODS

As a first illustration of the database, we present analyses of selected parameters on climate change, air pollution and flood risk for 64 cities in the WHO European Region.

RESULTS

Under a high greenhouse gas emissions trajectory (RCP8.5), the analyses suggest damaging temperature rises in European cities that are among the highest of any cities in the global database, while air pollution (PM_2.5) levels are appreciably above the WHO guideline level for all but a handful of cities. In several areas, these environmental hazards are compounded by flood risk.

DISCUSSION

Such evidence, though preliminary and based on limited data, underpins the need for urgent action on climate change (adaptation and mitigation) and risks relating to air pollution and other environmental hazards.

Symptomatic Dengue during Pregnancy and Congenital Neurologic Malformations

Dengue virus infection during pregnancy increased the risk for any neurologic congenital anomaly in the infant by roughly 50% and for other congenital malformations of brain 4-fold. Our results show an association between dengue during pregnancy and congenital anomalies of the brain, suggesting that flaviviruses other than Zika virus are associated with such malformations.

Effect of Early-Life Geohelminth Infections on the Development of Wheezing at 5 Years of Age

RATIONALE

Exposures to geohelminths during gestation or early childhood may reduce risk of wheezing illness/asthma and atopy during childhood in tropical regions.

OBJECTIVES

To investigate the effect of maternal and early childhood geohelminths on development of wheeze/asthma and atopy during the first 5 years of life.

METHODS

A cohort of 2,404 neonates was followed to 5 years of age in a rural district in coastal Ecuador. Data on wheeze were collected by questionnaire and atopy was measured by allergen skin prick test reactivity to 10 allergens at 5 years. Stool samples from mothers and children were examined for geohelminths by microscopy.

MEASUREMENTS AND MAIN RESULTS

A total of 2,090 (86.9%) children were evaluated at 5 years. Geohelminths were observed in 45.5% of mothers and in 34.1% of children by 3 years. Wheeze and asthma were reported for 12.6% and 5.7% of children, respectively, whereas 14.0% had skin test reactivity at 5 years. Maternal geohelminths were associated with an increased risk of wheeze (adjusted odds ratio, 1.41; 95% confidence interval, 1.06-1.88), whereas childhood geohelminths over the first 3 years of life were associated with reduced risk of wheeze (adjusted odds ratio, 0.70; 95% confidence interval, 0.52-0.96) and asthma (adjusted odds ratio, 0.60; 95% confidence interval, 0.38-0.94) but not skin prick test reactivity. The effects on wheeze/asthma were greatest with later age of first infection, were observed only in skin test-negative children, but were not associated with parasite burden or specific geohelminths.

CONCLUSIONS

Although maternal exposures to geohelminths may increase childhood wheeze, childhood geohelminths during the first 3 years may provide protection through a nonallergic mechanism. Registered as an observational study (ISRCTN41239086).

Effects of non-health-targeted policies on migrant health: a systematic review and meta-analysis

BACKGROUND

Government policies can strongly influence migrants' health. Using a Health in All Policies approach, we systematically reviewed evidence on the impact of public policies outside of the health-care system on migrant health.

METHODS

We searched the PubMed, Embase, and Web of Science databases from Jan 1, 2000, to Sept 1, 2017, for quantitative studies comparing the health effects of non-health-targeted public policies on migrants with those on a relevant comparison population. We searched for articles written in English, Swedish, Danish, Norwegian, Finnish, French, Spanish, or Portuguese. Qualitative studies and grey literature were excluded. We evaluated policy effects by migration stage (entry, integration, and exit) and by health outcome using narrative synthesis (all included studies) and random-effects meta-analysis (all studies whose results were amenable to statistical pooling). We summarised meta-analysis outcomes as standardised mean difference (SMD, 95% CI) or odds ratio (OR, 95% CI). To assess certainty, we created tables containing a summary of the findings according to the Grading of Recommendations Assessment, Development, and Evaluation. Our study was registered with PROSPERO, number CRD42017076104.

FINDINGS

We identified 43 243 potentially eligible records. 46 articles were narratively synthesised and 19 contributed to the meta-analysis. All studies were published in high-income countries and examined policies of entry (nine articles) and integration (37 articles). Restrictive entry policies (eg, temporary visa status, detention) were associated with poor mental health (SMD 0·44, 95% CI 0·13-0·75; I2=92·1%). In the integration phase, restrictive policies in general, and specifically regarding welfare eligibility and documentation requirements, were found to increase odds of poor self-rated health (OR 1·67, 95% CI 1·35-1·98; I2=82·0%) and mortality (1·38, 1·10-1·65; I2=98·9%). Restricted eligibility for welfare support decreased the odds of general health-care service use (0·92, 0·85-0·98; I2=0·0%), but did not reduce public health insurance coverage (0·89, 0·71-1·07; I2=99·4%), nor markedly affect proportions of people without health insurance (1·06, 0·90-1·21; I2=54·9%).

INTERPRETATION

Restrictive entry and integration policies are linked to poor migrant health outcomes in high-income countries. Efforts to improve the health of migrants would benefit from adopting a Health in All Policies perspective.

FUNDING

Swedish Council for Health, Working Life, and Social Research; UK Medical Research Council; Scottish Government Chief Scientist Office.

The impact of a cash transfer programme on tuberculosis treatment success rate: a quasi-experimental study in Brazil

Background

Evidence suggests that social protection policies such as Brazil’s Bolsa Família Programme (BFP), a governmental conditional cash transfer, may play a role in tuberculosis (TB) elimination. However, study limitations hamper conclusions. This paper uses a quasi-experimental approach to more rigorously evaluate the effect of BFP on TB treatment success rate.

Methods

Propensity scores were estimated from a complete-case logistic regression using covariates from a linked data set, including the Brazil’s TB notification system (SINAN), linked to the national registry of those in poverty (CadUnico) and the BFP payroll.

Results

The average effect of treatment on the treated was estimated as the difference in TB treatment success rate between matched groups (ie, the control and exposed patients, n=2167). Patients with TB receiving BFP showed a treatment success rate of 10.58 percentage points higher (95% CI 4.39 to 16.77) than patients with TB not receiving BFP. This association was robust to sensitivity analyses.

Conclusions

This study further confirms a positive relationship between the provision of conditional cash transfers and TB treatment success rate. Further research is needed to understand how to enhance access to social protection so to optimise public health impact.

On the Accuracy and Scalability of Probabilistic Data Linkage Over the Brazilian 114 Million Cohort

Data linkage refers to the process of identifying and linking records that refer to the same entity across multiple heterogeneous data sources. This method has been widely utilized across scientific domains, including public health where records from clinical, administrative, and other surveillance databases are aggregated and used for research, decision making, and assessment of public policies. When a common set of unique identifiers does not exist across sources, probabilistic linkage approaches are used to link records using a combination of attributes. These methods require a careful choice of comparison attributes as well as similarity metrics and cutoff values to decide if a given pair of records matches or not and for assessing the accuracy of the results. In large, complex datasets, linking and assessing accuracy can be challenging due to the volume and complexity of the data, the absence of a gold standard, and the challenges associated with manually reviewing a very large number of record matches. In this paper, we present AtyImo, a hybrid probabilistic linkage tool optimized for high accuracy and scalability in massive data sets. We describe the implementation details around anonymization, blocking, deterministic and probabilistic linkage, and accuracy assessment. We present results from linking a large population-based cohort of 114 million individuals in Brazil to public health and administrative databases for research. In controlled and real scenarios, we observed high accuracy of results: 93%-97% true matches. In terms of scalability, we present AtyImo’s ability to link the entire cohort in less than nine days using Spark and scaling up to 20 million records in less than 12s over heterogeneous (CPU+GPU) architectures.

The UCL-Lancet Commission on Migration and Health: the health of a world on the move

With one billion people on the move or having moved in 2018, migration is a global reality, which has also become a political lightning rod. Although estimates indicate that the majority of global migration occurs within low-income and middle-income countries (LMICs), the most prominent dialogue focuses almost exclusively on migration from LMICs to high-income countries (HICs). Nowadays, populist discourse demonises the very same individuals who uphold economies, bolster social services, and contribute to health services in both origin and destination locations. Those in positions of political and economic power continue to restrict or publicly condemn migration to promote their own interests. Meanwhile nationalist movements assert so-called cultural sovereignty by delineating an us versus them rhetoric, creating a moral emergency.

In response to these issues, the UCL-Lancet Commission on Migration and Health was convened to articulate evidence-based approaches to inform public discourse and policy. The Commission undertook analyses and consulted widely, with diverse international evidence and expertise spanning sociology, politics, public health science, law, humanitarianism, and anthropology. The result of this work is a report that aims to be a call to action for civil society, health leaders, academics, and policy makers to maximise the benefits and reduce the costs of migration on health locally and globally. The outputs of our work relate to five overarching goals that we thread throughout the report.

First, we provide the latest evidence on migration and health outcomes. This evidence challenges common myths and highlights the diversity, dynamics, and benefits of modern migration and how it relates to population and individual health. Migrants generally contribute more to the wealth of host societies than they cost. Our Article shows that international migrants in HICs have, on average, lower mortality than the host country population. However, increased morbidity was found for some conditions and among certain subgroups of migrants, (eg, increased rates of mental illness in victims of trafficking and people fleeing conflict) and in populations left behind in the location of origin. Currently, in 2018, the full range of migrants’ health needs are difficult to assess because of poor quality data. We know very little, for example, about the health of undocumented migrants, people with disabilities, or lesbian, gay, bisexual, transsexual, or intersex (LGBTI) individuals who migrate or who are unable to move.

Second, we examine multisector determinants of health and consider the implication of the current sector-siloed approaches. The health of people who migrate depends greatly on structural and political factors that determine the impetus for migration, the conditions of their journey, and their destination. Discrimination, gender inequalities, and exclusion from health and social services repeatedly emerge as negative health influences for migrants that require cross-sector responses.

Third, we critically review key challenges to healthy migration. Population mobility provides economic, social, and cultural dividends for those who migrate and their host communities. Furthermore, the right to the highest attainable standard of health, regardless of location or migration status, is enshrined in numerous human rights instruments. However, national sovereignty concerns overshadow these benefits and legal norms. Attention to migration focuses largely on security concerns. When there is conjoining of the words health and migration, it is either focused on small subsets of society and policy, or negatively construed. International agreements, such as the UN Global Compact for Migration and the UN Global Compact on Refugees, represent an opportunity to ensure that international solidarity, unity of intent, and our shared humanity triumphs over nationalist and exclusionary policies, leading to concrete actions to protect the health of migrants.

Fourth, we examine equity in access to health and health services and offer evidence-based solutions to improve the health of migrants. Migrants should be explicitly included in universal health coverage commitments. Ultimately, the cost of failing to be health-inclusive could be more expensive to national economies, health security, and global health than the modest investments required.

Finally, we look ahead to outline how our evidence can contribute to synergistic and equitable health, social, and economic policies, and feasible strategies to inform and inspire action by migrants, policy makers, and civil society. We conclude that migration should be treated as a central feature of 21st century health and development. Commitments to the health of migrating populations should be considered across all Sustainable Development Goals (SDGs) and in the implementation of the Global Compact for Migration and Global Compact on Refugees. This Commission offers recommendations that view population mobility as an asset to global health by showing the meaning and reality of good health for all. We present four key messages that provide a focus for future action.

Area deprivation measures used in Brazil: a scoping review

OBJECTIVE

To describe and assess currently used area-based measures of deprivation in Brazil for health research, to the purpose of informing the development of a future small area deprivation index.

METHODS

We searched five electronic databases and seven websites of Brazilian research institutions and governmental agencies. Inclusion criteria were: studies proposing measures of deprivation for small areas (i.e., finer geography than country-level) in Brazil, published in English, Portuguese or Spanish. After data-extraction, results were tabulated according to the area level the deprivation measure was created for and to the dimensions of deprivation or poverty included in the measures. A narrative synthesis approach was used to summarize the measures available, highlighting their utility for public health research.

RESULTS

A total of 7,199 records were retrieved, 126 full-text articles were assessed after inclusion criteria and a final list of 30 articles was selected. No small-area deprivation measures that have been applied to the whole of Brazil were found. Existing measures were mainly used to study infectious and parasitic diseases. Few studies used the measures to assess inequalities in mortality and no studies used the deprivation measure to evaluate the impact of social programs.

CONCLUSIONS

No up-to-date small area-based deprivation measure in Brazil covers the whole country. There is a need to develop such an index for Brazil to measure and monitor inequalities in health and mortality, particularly to assess progress in Brazil against the Sustainable Development Goal targets for different health outcomes, showing progress by socioeconomic groups.

Burden of disease in Brazil, 1990-2016: a systematic subnational analysis for the Global Burden of Disease Study 2016

BACKGROUND

Political, economic, and epidemiological changes in Brazil have affected health and the health system. We used the Global Burden of Disease Study 2016 (GBD 2016) results to understand changing health patterns and inform policy responses.

METHODS

We analysed GBD 2016 estimates for life expectancy at birth (LE), healthy life expectancy (HALE), all-cause and cause-specific mortality, years of life lost (YLLs), years lived with disability (YLDs), disability-adjusted life-years (DALYs), and risk factors for Brazil, its 26 states, and the Federal District from 1990 to 2016, and compared these with national estimates for ten comparator countries.

FINDINGS

Nationally, LE increased from 68·4 years (95% uncertainty interval [UI] 68·0-68·9) in 1990 to 75·2 years (74·7-75·7) in 2016, and HALE increased from 59·8 years (57·1-62·1) to 65·5 years (62·5-68·0). All-cause age-standardised mortality rates decreased by 34·0% (33·4-34·5), while all-cause age-standardised DALY rates decreased by 30·2% (27·7-32·8); the magnitude of declines varied among states. In 2016, ischaemic heart disease was the leading cause of age-standardised YLLs, followed by interpersonal violence. Low back and neck pain, sense organ diseases, and skin diseases were the main causes of YLDs in 1990 and 2016. Leading risk factors contributing to DALYs in 2016 were alcohol and drug use, high blood pressure, and high body-mass index.

INTERPRETATION

Health improved from 1990 to 2016, but improvements and disease burden varied between states. An epidemiological transition towards non-communicable diseases and related risks occurred nationally, but later in some states, while interpersonal violence grew as a health concern. Policy makers can use these results to address health disparities.

FUNDING

Bill & Melinda Gates Foundation and the Brazilian Ministry of Health.

Understanding asthma phenotypes: the World Asthma Phenotypes (WASP) international collaboration

The World Asthma Phenotypes (WASP) study started in 2016 and has been conducted in five centres, in the UK, New Zealand, Brazil, Ecuador and Uganda. The objectives of this study are to combine detailed biomarker and clinical information in order to 1) better understand and characterise asthma phenotypes in high-income countries (HICs) and low and middle-income countries (LMICs), and in high and low prevalence centres; 2) compare phenotype characteristics, including clinical severity; 3) assess the risk factors for each phenotype; and 4) assess how the distribution of phenotypes differs between high prevalence and low prevalence centres. Here we present the rationale and protocol for the WASP study to enable other centres around the world to carry out similar analyses using a standardised protocol. Large collaborative and integrative studies like this are essential to further our understanding of asthma phenotypes. The findings of this study will help elucidate the aetiological mechanisms of asthma and might potentially identify new causes and guide the development of new treatments, thereby enabling better management and prevention of asthma in both HICs and LMICs.

Dengue in pregnancy and maternal mortality: a cohort analysis using routine data

Dengue is a mosquito-borne disease with major public health importance due to its growing incidence and geographical spread. There is a lack of knowledge on its contribution to maternal death. We conducted a population-based cohort study to investigate the association between symptomatic dengue during pregnancy and deaths in Brazil from 2007 to 2012. We did this by linking routine records of confirmed dengue cases to records of deaths of women who had a live birth. Using the Firth method, we estimated odds ratios for maternal deaths associated with dengue during pregnancy. Dengue increased the risk of maternal death by 3 times (95%CI,1.5-5.8) and dengue haemorrhagic fever increased the risk of maternal death by 450 times (95%CI,186.9-1088.4) when compared to mortality of pregnant women without dengue. The increase in risk occurred mostly during acute dengue 71.5 (95%CI,32.8-155.8), compared with no dengue cases. This study showed an increased risk of adverse outcomes in pregnant women with dengue. Therefore in areas where dengue is circulating, the health of pregnant women should be not only a public health priority, but health professionals attending pregnant women with dengue should more closely observe these patients to be able to intervene in a timely way and avoid deaths.

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel—the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs (info score ≥ 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources.

Genetic structure of pharmacogenetic biomarkers in Brazil inferred from a systematic review and population-based cohorts: a RIBEF/EPIGEN-Brazil initiative

We present allele frequencies involving 39 pharmacogenetic biomarkers studied in Brazil, and their distribution on self-reported race/color categories that: (1) involve a mix of perceptions about ancestry, morphological traits, and cultural/identity issues, being social constructs pervasively used in Brazilian society and medical studies; (2) are associated with disparities in access to health services, as well as in their representation in genetic studies, and (3), as we report here, explain a larger portion of the variance of pharmaco-allele frequencies than geography. We integrated a systematic review of studies on healthy volunteers (years 1968-2017) and the analysis of allele frequencies on three population-based cohorts from northeast, southeast, and south, the most populated regions of Brazil. Cross-validation of results from these both approaches suggest that, despite methodological heterogeneity of the 120 studies conducted on 51,747 healthy volunteers, allele frequencies estimates from systematic review are reliable. We report differences in allele frequencies between color categories that persist despite the homogenizing effect of >500 years of admixture. Among clinically relevant variants: CYP2C9*2 (null), CYP3A5*3 (defective), SLCO1B1-rs4149056(C), and VKORC1-rs9923231(A) are more frequent in Whites than in Blacks. Brazilian Native Americans show lower frequencies of CYP2C9*2, CYP2C19*17 (increased activity), and higher of SLCO1B1-rs4149056(C) than other Brazilian populations. We present the most current and informative database of pharmaco-allele frequencies in Brazilian healthy volunteers.

Challenges in administrative data linkage for research

Linkage of population-based administrative data is a valuable tool for combining detailed individual-level information from different sources for research. While not a substitute for classical studies based on primary data collection, analyses of linked administrative data can answer questions that require large sample sizes or detailed data on hard-to-reach populations, and generate evidence with a high level of external validity and applicability for policy making. There are unique challenges in the appropriate research use of linked administrative data, for example with respect to bias from linkage errors where records cannot be linked or are linked together incorrectly. For confidentiality and other reasons, the separation of data linkage processes and analysis of linked data is generally regarded as best practice. However, the 'black box' of data linkage can make it difficult for researchers to judge the reliability of the resulting linked data for their required purposes. This article aims to provide an overview of challenges in linking administrative data for research. We aim to increase understanding of the implications of (i) the data linkage environment and privacy preservation; (ii) the linkage process itself (including data preparation, and deterministic and probabilistic linkage methods) and (iii) linkage quality and potential bias in linked data. We draw on examples from a number of countries to illustrate a range of approaches for data linkage in different contexts.

Symptomatic dengue infection during pregnancy and the risk of stillbirth in Brazil, 2006-12: a matched case-control study

BACKGROUND

Maternal infections during pregnancy can increase the risk of fetal death. Dengue infection is common, but little is known about its role in fetal mortality. We aimed to investigate the association between symptomatic dengue infection during pregnancy and fetal death.

METHODS

We did a nested case-control study using obstetrician-collected data from the Brazilian livebirth information system (SINASC), the mortality information system (SIM), and the national reportable disease information system (SINAN). We identified all pregnancies ending in stillbirth and a random sample of livebirths between Jan 1, 2006, and Dec 31, 2012. We did linkage to determine which mothers were diagnosed with dengue infection during pregnancy. By use of stillbirths as cases and a sample of matched livebirths as a control, we calculated matched odds ratios (mORs) using conditional logistic regression adjusted for maternal age and education.

FINDINGS

275 (0·2%) of 162 188 women who had stillbirths and 1507 (0·1%) of 1 586 105 women who had livebirths were diagnosed with dengue infection during pregnancy. Symptomatic dengue infection during pregnancy almost doubled the odds of fetal death (mOR 1·9, 95% CI 1·6-2·2). The increase in risk was similar when analyses were restricted to laboratory-confirmed cases of dengue infection (1·8, 1·4-2·4). Severe dengue infection increased the risk of fetal death by about five times (4·9, 2·3-10·2).

INTERPRETATION

Symptomatic dengue infection during pregnancy is associated with an increased risk of fetal death. We recommend further epidemiological and biological studies of the association between dengue and poor birth outcomes to measure the burden of subclinical infections and elucidate pathological mechanisms.

FUNDING

Brazilian National Council for Scientific and Technological Development, Horizon 2020.

Growth patterns in early childhood: Better trajectories in Afro-Ecuadorians independent of sex and socioeconomic factors

The first years of life are the most dynamic period for childhood growth. There are limited data available on growth patterns of infants and children living in rural Latin America. The aim of this study was to describe the growth patterns from birth to 5years in children living in a rural District of tropical coastal Ecuador using data from a birth cohort of 2404 neonates. We hypothesize that there would be growth differences according to ethnicity and sex. Evaluations were conducted at birth or until 2weeks of age and at 7, 13, 24, 36 and 60months during clinic and home visits. Individual growth trajectories for weight-for-age, height-for-age and weight/height-for-age Z-scores were estimated using multilevel models. Girls were lighter and shorter than boys at birth. However, Afro-Ecuadorian children (versus mestizo or indigenous) were longer/taller and heavier throughout the first 5years of life and had greater mean trajectories for HAZ and WAZ independent of sex and socioeconomic factors. Our data indicate that ethnicity is a determinant of growth trajectories during the first 5years of life independent of socioeconomic factors in a birth cohort conducted in a rural region of Latin America.