Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling.

Introduction: Neoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow. Methods: In this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). Immunogenicity was then validated by ELISpot assay using long synthesis peptides (sLP). Results: We detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data. Discussion: This integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients.

An adaptive weighting mechanism for Reynolds rules-based flocking control scheme.

Cooperative navigation for fleets of robots conventionally adopts algorithms based on Reynolds's flocking rules, which usually use a weighted sum of vectors for calculating the velocity from behavioral velocity vectors with corresponding fixed weights. Although optimal values of the weighting coefficients giving good performance can be found through many experiments for each particular scenario, the overall performance could not be guaranteed due to unexpected conditions not covered in experiments. This paper proposes a novel control scheme for a swarm of Unmanned Aerial Vehicles (UAVs) that also employs the original Reynolds rules but adopts an adaptive weight allocation mechanism based on the current context than being fixed at the beginning. The simulation results show that our proposed scheme has better performance than the conventional Reynolds-based ones in terms of the flock compactness and the reduction in the number of crashed swarm members due to collisions. The analytical results of behavioral rules' impact also validate the proposed weighting mechanism's effectiveness leading to improved performance.