Department of Mathematics and Computer Science

Rare diseases affect a small proportion of the population, often characterized by complex, variable, and sometimes poorly understood symptoms, limited treatment options, and significant impacts on patients’ daily lives. Human phenotypes refer to the observable characteristics or traits of an individual, encompassing physical, behavioral, and biochemical features that can result from the interaction of genetic and environmental factors. Studying phenotypes is crucial in rare disease research, as it helps link symptoms to their underlying genetic causes.

Supporting rare disease genomics and precision medicine [1], the Human Phenotype Ontology (HPO) provides a standardized corpus of over 8,100 rare disease phenotype annotations (see [2]). HPO is widely used in clinical genetics tools, such as Exomiser, LIRICAL, SimulConsult, PhenoTips, and Face2Gene [3]. While these tools effectively support genomic variant classification (e.g., [4]), there is limited research on user interfaces that enable laypersons to explore rare disease phenotypes, focusing on intuitive interaction patterns and accessible language [5]. Consequently, laypersons may struggle to interact with phenotype data, which can limit their comprehension and engagement. Leveraging HPO and human phenotypes within an HCI framework could enhance understanding of the relationships between phenotypic traits and rare diseases.

Objectives

• Analysis of tools and approaches in HCI and human phenotype exploration.
• Development of a Figma prototype for interactive exploration of rare disease phenotypes, considering a concrete rare disease scenario,
• Evaluation of the usability of the prototype through heuristic analysis with lay users.

Procedure

1. Conduct an in-depth analysis of HPO-based applications (e.g., Face2Gene, PhenoTips) and a state-of-the-art literature review on HCI tools and approaches (e.g., [6, 7, 8, 9, 10]) for disease exploration. Based on the insights, define design criteria for visual and interactive prototyping.
2. Define a specific rare disease scenario and extract relevant phenotype annotations from HPO that further help to define the requirements for prototype development.
3. Consider insights from (1) and (2) to design an interactive Figma prototype based on HPO data and HCI approaches.
4. Evaluate the prototype through heuristic analysis with lay users to assess its usability.
5. Document findings and discuss recommendations for future tools to explore human phenotypes in rare disease.

References

[1] Hong, J., Lee, D., Hwang, A., Kim, T., Ryu, H. Y., & Choi, J. (2024). Rare disease genomics and precision medicine. Genomics & Informatics, 22(1), 28. https://doi.org/10.1186/s44342-024-00032-1
[2] Human Phenotype Ontology. (n.d.). The Jackson Laboratory. https://hpo.jax.org/
[3] Talapova, P. et al. (2023). The Human Phenotype Ontology in 2024: phenotypes around the world. https://doi.org/10.1093/nar/gkad1005
[4] Bauer, S., Grossmann, S., Vingron, M., & Robinson, P. N. (2008). Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24(14), 1650-1651. https://doi.org/10.1093/bioinformatics/btn250
[5] Vasilevsky, N. A., Engelstad, M., Foster, E. D., Mungall, C. J., Robinson, P. N., Köhler, S., & Haendel, M. A. (2016). Enhancing the human phenotype ontology for use by the layperson. https://hdl.handle.net/1805/21027
[6] Shaer, O., Nov, O., Okerlund, J., Balestra, M., Stowell, E., Westendorf, L., Pollalis, C., Davix, J., Westort, L., & Ball, M. (2016, May). Genomix: A novel interaction tool for self-exploration of personal genomic data. In Proceedings of the 2016 CHI Conference on Human Factors in Computing Systems (pp. 661-672). https://doi.org/10.1145/2858036.2858397
[7] MacLeod, H., Bastin, G., Liu, L. S., Siek, K., & Connelly, K. (2017, May). " Be Grateful You Don't Have a Real Disease" Understanding Rare Disease Relationships. In Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems (pp. 1660-1673). https://doi.org/10.1145/3025453.3025796
[8] Nielsen, E. E., Owen, T., Roach, M., & Dix, A. (2023, April). A Patient Centred Approach to Rare Disease Technology. In Extended Abstracts of the 2023 CHI Conference on Human Factors in Computing Systems (pp. 1-7). https://doi.org/10.1145/3544549.3585826
[9] Shaer, O., Nov, O., West, A., & Eastman, D. (2014). Understanding information practices of interactive personal genomics users. In CHI'14 Extended Abstracts on Human Factors in Computing Systems (pp. 2455-2460). http://dx.doi.org/10.1145/2559206.2581145
[10] Zhou, Y., Kamruzzaman, M., Schnable, P., Krishnamoorthy, B., Kalyanaraman, A., & Wang, B. (2021, August). Pheno-Mapper: an interactive toolbox for the visual exploration of phenomics data. In Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 1-10). https://doi.org/10.1145/3459930.3469511