Functional annotation of human long noncoding RNAs via molecular phenotyping.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

Quantitative bias analysis in practice: review of software for regression with unmeasured confounding.

BACKGROUND: Failure to appropriately account for unmeasured confounding may lead to erroneous conclusions. Quantitative bias analysis (QBA) can be used to quantify the potential impact of unmeasured confounding or how much unmeasured confounding would be needed to change a study's conclusions. Currently, QBA methods are not routinely implemented, partly due to a lack of knowledge about accessible software. Also, comparisons of QBA methods have focused on analyses with a binary outcome. METHODS: We conducted a systematic review of the latest developments in QBA software published between 2011 and 2021. Our inclusion criteria were software that did not require adaption (i.e., code changes) before application, was still available in 2022, and accompanied by documentation. Key properties of each software tool were identified. We provide a detailed description of programs applicable for a linear regression analysis, illustrate their application using two data examples and provide code to assist researchers in future use of these programs. RESULTS: Our review identified 21 programs with [Formula: see text] created post 2016. All are implementations of a deterministic QBA with [Formula: see text] available in the free software R. There are programs applicable when the analysis of interest is a regression of binary, continuous or survival outcomes, and for matched and mediation analyses. We identified five programs implementing differing QBAs for a continuous outcome: treatSens, causalsens, sensemakr, EValue, and konfound. When applied to one of our illustrative examples, causalsens incorrectly indicated sensitivity to unmeasured confounding whereas the other four programs indicated robustness. sensemakr performs the most detailed QBA and includes a benchmarking feature for multiple unmeasured confounders. CONCLUSIONS: Software is now available to implement a QBA for a range of different analyses. However, the diversity of methods, even for the same analysis of interest, presents challenges to their widespread uptake. Provision of detailed QBA guidelines would be highly beneficial.

Exploring the impact of selection bias in observational studies of COVID-19: a simulation study.

BACKGROUND: Non-random selection of analytic subsamples could introduce selection bias in observational studies. We explored the potential presence and impact of selection in studies of SARS-CoV-2 infection and COVID-19 prognosis. METHODS: We tested the association of a broad range of characteristics with selection into COVID-19 analytic subsamples in the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK Biobank (UKB). We then conducted empirical analyses and simulations to explore the potential presence, direction and magnitude of bias due to this selection (relative to our defined UK-based adult target populations) when estimating the association of body mass index (BMI) with SARS-CoV-2 infection and death-with-COVID-19. RESULTS: In both cohorts, a broad range of characteristics was related to selection, sometimes in opposite directions (e.g. more-educated people were more likely to have data on SARS-CoV-2 infection in ALSPAC, but less likely in UKB). Higher BMI was associated with higher odds of SARS-CoV-2 infection and death-with-COVID-19. We found non-negligible bias in many simulated scenarios. CONCLUSIONS: Analyses using COVID-19 self-reported or national registry data may be biased due to selection. The magnitude and direction of this bias depend on the outcome definition, the true effect of the risk factor and the assumed selection mechanism; these are likely to differ between studies with different target populations. Bias due to sample selection is a key concern in COVID-19 research based on national registry data, especially as countries end free mass testing. The framework we have used can be applied by other researchers assessing the extent to which their results may be biased for their research question of interest.

Genetic regulation of fetal hemoglobin across global populations.

Human genetic variation has enabled the identification of several key regulators of fetal-to-adult hemoglobin switching, including BCL11A, resulting in therapeutic advances. However, despite the progress made, limited further insights have been obtained to provide a fuller accounting of how genetic variation contributes to the global mechanisms of fetal hemoglobin (HbF) gene regulation. Here, we have conducted a multi-ancestry genome-wide association study of 28,279 individuals from several cohorts spanning 5 continents to define the architecture of human genetic variation impacting HbF. We have identified a total of 178 conditionally independent genome-wide significant or suggestive variants across 14 genomic windows. Importantly, these new data enable us to better define the mechanisms by which HbF switching occurs in vivo. We conduct targeted perturbations to define BACH2 as a new genetically-nominated regulator of hemoglobin switching. We define putative causal variants and underlying mechanisms at the well-studied BCL11A and HBS1L-MYB loci, illuminating the complex variant-driven regulation present at these loci. We additionally show how rare large-effect deletions in the HBB locus can interact with polygenic variation to influence HbF levels. Our study paves the way for the next generation of therapies to more effectively induce HbF in sickle cell disease and ß-thalassemia.

The effects of introducing electric adjustable height desks in an office setting on workplace physical activity levels: A randomised control field trial.

BACKGROUND: Electric adjustable height desks (EAHD) have been promoted as an opportunity for desk based workers to stand at work but there is limited evidence that they have an effect on light physical activity. OBJECTIVE: The main objective was to determine if there would be a change in light physical activity with the introduction of EAHD. The secondary objective was to assess if there was an associated change in leisure time activity. METHODS: Activity levels were measured by step counts, self-reported activity levels and pre- and post-trial recall levels. Statistical analysis of the data was performed with the software R. Generalised linear models were fitted to the data. A Poisson regression was used for count data. Statistical hypotheses were deemed significant if their p values were less than 0.05. RESULTS: There was a significant (p < 0.001) effect on step counts associated with allocation of EAHD and a significant (p < 0.001) increase in self-reported activity for the Intervention (EAHD) group. Having an EAHD was associated with increased activity during leisure (p = 0.039). CONCLUSIONS: Activity levels, especially light physical activity, were significantly increased with the allocation of an electric adjustable height desk. This pilot study showed that the environmental change of introduction of electric adjustable height desks into an office workplace can increase physical activity and reduce sitting durations. There is limited evidence that the increase in work activity has a positive impact on leisure time activity.