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Simple Summary: Genome-wide association studies (GWAS) are a powerful tool for the identification of genes affecting human traits. Still, the interpretation of GWAS results is complicated, and new tools are actively being developed. Due to the scarcity of available datasets, simulation of GWAS data with known genetic effects is important as it enables accurate evaluation of such tools. In this study, we developed a flexible tool, bioGWAS, that provides a set of important functionalities for simulating GWAS results. We demonstrate that bioGWAS can efficiently generate GWAS results with predefined causal genes and biological processes and is capable of recapitulating the results of published GWAS studies. We thus believe that bioGWAS is an excellent method for testing bioinformatics software for GWAS results processing, as well as for the generation of datasets for educational purposes. Genome-wide association studies (GWAS) have proven to be a powerful tool for the identification of genetic susceptibility loci affecting human complex traits. In addition to pinpointing individual genes involved in a particular trait, GWAS results can be used to discover relevant biological processes for these traits. The development of new tools for extracting such information from GWAS results requires large-scale datasets with known biological ground truth. Simulation of GWAS results is a powerful method that may provide such datasets and facilitate the development of new methods. In this work, we developed bioGWAS, a simple and flexible pipeline for the simulation of genotypes, phenotypes, and GWAS summary statistics. Unlike existing methods, bioGWAS can be used to generate GWAS results for simulated quantitative and binary traits with a predefined set of causal genetic variants and/or molecular pathways. We demonstrate that the proposed method can recapitulate complete GWAS datasets using a set of reported genome-wide associations. We also used our method to benchmark several tools for gene set enrichment analysis for GWAS data. Taken together, our results suggest that bioGWAS provides an important set of functionalities that would aid the development of new methods for downstream processing of GWAS results. [ABSTRACT FROM AUTHOR]

Simple Summary: Prions are self-perpetuating protein aggregates that cause fatal neurodegenerative diseases in humans and other mammalian species. In yeast, in contrast to mammals, prions can be maintained in the cell population and confer adaptive traits. Fluorescence microscopy is commonly used to visualize prion aggregates in living cells, providing important information regarding the morphology and localization of prion particles in the cell. In most studies, various constructs with green fluorescent protein (GFP) are used to detect particles of the most-studied yeast prion, [PSI+]. In our work, we tried to substitute GFP with two different red fluorescent protein variants to expand the application of prion particle imaging. Surprisingly, we found that the processing of the fluorescently labeled prionogenic protein can prevent the detection of prion particles. This pattern was observed for one of the studied red fluorescent proteins (mCherry) and was not dependent on any tested protein degradation systems. The present work thus highlights the limitations of aggregate labeling with fluorescent proteins and suggests labeling with mCherry should be avoided. Yeast is a convenient model for studying protein aggregation as it is known to propagate amyloid prions. [PSI+] is the prion form of the release factor eRF3 (Sup35). Aggregated Sup35 causes defects in termination of translation, which results in nonsense suppression in strains carrying premature stop codons. N-terminal and middle (M) domains of Sup35 are necessary and sufficient for maintaining [PSI+] in cells while preserving the prion strain's properties. For this reason, Sup35NM fused to fluorescent proteins is often used for [PSI+] detection and investigation. However, we found that in such chimeric constructs, not all fluorescent proteins allow the reliable detection of Sup35 aggregates. Particularly, transient overproduction of Sup35NM-mCherry resulted in a diffuse fluorescent pattern in the [PSI+] cells, while no loss of prions and no effect on the Sup35NM prion properties could be observed. This effect was reproduced in various unrelated strain backgrounds and prion variants. In contrast, Sup35NM fused to another red fluorescent protein, TagRFP-T, allowed the detection of [PSI+] aggregates. Analysis of protein lysates showed that Sup35NM-mCherry is actively degraded in the cell. This degradation was not caused by vacuolar proteases and the ubiquitin-proteasomal system implicated in the Sup35 processing. Even though the intensity of this proteolysis was higher than that of Sup35NM-GFP, it was roughly the same as in the case of Sup35NM-TagRFP-T. Thus, it is possible that, in contrast to TagRFP-T, degradation products of Sup35NM-mCherry still preserve their fluorescent properties while losing the ability to decorate pre-existing Sup35 aggregates. This results in diffuse fluorescence despite the presence of the prion aggregates in the cell. Thus, tagging with fluorescent proteins should be used with caution, as such proteolysis may increase the rate of false-negative results when detecting prion-bearing cells. [ABSTRACT FROM AUTHOR]