Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens.

Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.

Correction: Ethical Issues in Social Media Recruitment for Clinical Studies: Ethical Analysis and Framework.

[This corrects the article DOI: 10.2196/31231.].

Ethical Issues in Social Media Recruitment for Clinical Studies: Ethical Analysis and Framework.

BACKGROUND: Social media recruitment for clinical studies holds the promise of being a cost-effective way of attracting traditionally marginalized populations and promoting patient engagement with researchers and a particular study. However, using social media for recruiting clinical study participants also poses a range of ethical issues. OBJECTIVE: This study aims to provide a comprehensive overview of the ethical benefits and risks to be considered for social media recruitment in clinical studies and develop practical recommendations on how to implement these considerations. METHODS: On the basis of established principles of clinical ethics and research ethics, we reviewed the conceptual and empirical literature for ethical benefits and challenges related to social media recruitment. From these, we derived a conceptual framework to evaluate the eligibility of social media use for recruitment for a specific clinical study. RESULTS: We identified three eligibility criteria for social media recruitment for clinical studies: information and consent, risks for target groups, and recruitment effectiveness. These criteria can be used to evaluate the implementation of a social media recruitment strategy at its planning stage. We have discussed the practical implications of these criteria for researchers. CONCLUSIONS: The ethical challenges related to social media recruitment are context sensitive. Therefore, social media recruitment should be planned rigorously, taking into account the target group, the appropriateness of social media as a recruitment channel, and the resources available to execute the strategy.