A course-undergraduate research experience (CURE) to explore the effect of structural variants on gene expression in...

Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches. Yet, the undergraduate programs offering such multidisciplinary training are rare. In addition, understanding the interplay between Biology research projects and Bioinformatics analyses is challenging without hands-on experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences at the Cumming School of Medicine, University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter semesters of 2023-2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. The students used Galaxy, a public web-based super-computing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Beyond acquiring new skills, students uncovered new findings, such as effects of a reciprocal translocation eT1(III;V) on gene expression of H14N18.2. We obtained data on the course's impact on student learning journeys by administering a voluntary student-based survey with 14% response rate (standard response rate at the University of Calgary). Overall, the available data survey showed that CURE facilitated students understanding of the Bioinformatics field and fostered their research interest. Beyond these results, we provide here guidelines on facilitating similar CURE implementations to improve access to bioinformatics research experiences for undergraduate students.