Spatial Bayesian distributed lag non-linear models (SB-DLNM) for small-area exposure-lag-response epidemiological modelling

BACKGROUND

Distributed lag non-linear models (DLNMs) are the reference framework for modelling lagged non-linear associations. They are usually used in large-scale multi-location studies. Attempts to study these associations in small areas either did not include the lagged non-linear effects, did not allow for geographically-varying risks or downscaled risks from larger spatial units through socioeconomic and physical meta-predictors when the estimation of the risks was not feasible due to low statistical power.

METHODS

Here we proposed spatial Bayesian DLNMs (SB-DLNMs) as a new framework for the estimation of reliable small-area lagged non-linear associations, and demonstrated the methodology for the case study of the temperature-mortality relationship in the 73 neighbourhoods of the city of Barcelona. We generalized location-independent DLNMs to the Bayesian framework (B-DLNMs), and extended them to SB-DLNMs by incorporating spatial models in a single-stage approach that accounts for the spatial dependence between risks.

RESULTS

The results of the case study highlighted the benefits of incorporating the spatial component for small-area analysis. Estimates obtained from independent B-DLNMs were unstable and unreliable, particularly in neighbourhoods with very low numbers of deaths. SB-DLNMs addressed these instabilities by incorporating spatial dependencies, resulting in more plausible and coherent estimates and revealing hidden spatial patterns. In addition, the Bayesian framework enriches the range of estimates and tests that can be used in both large- and small-area studies.

CONCLUSIONS

SB-DLNMs account for spatial structures in the risk associations across small areas. By modelling spatial differences, SB-DLNMs facilitate the direct estimation of non-linear exposure-response lagged associations at the small-area level, even in areas with as few as 19 deaths. The manuscript includes an illustrative code to reproduce the results, and to facilitate the implementation of other case studies by other researchers.

The European Nucleotide Archive in 2023

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.