Call for use cases: Cytogenetics

[ahwagner]

Call for Use Cases: Representing Cytogenetic Knowledge

We’d like to gather community input on use cases for representing cytogenetic knowledge in VRS. This will help us better understand current challenges and opportunities for developing the standard as part of an interoperable ecosystem of tools that share information about cytogenetic assays and related knowledge.

Problem Statement

• Comparing across cytogenomic and molecular results is currently challenging.
• Cytogenomic nomenclature does not natively represent results as discrete, searchable components.
• Cytogenomic data structures are being re-engineered as customized implementations across large-scale knowledge management systems
• Much of this knowledge from smaller organizations remains siloed in unstructured or semi-structured formats (Excel spreadsheets, Word documents, etc.) in clinical settings due to a lack of standardized, easy-to-use representation tools

Relevant Resources

These established knowledge providers highlight the need for structured representations of cytogenetic results and knowledge:

• Atlas of Genetics and Cytogenetics in Oncology and Haematology
• Mitelman Database of Chromosome Aberrations and Gene Fusions
• HGNC and [ClinVar], which use cytoband locations in their data models

We’d love to hear from you!

Please share:

• Specific use cases you encounter when working with cytogenetic results or knowledge.
• Examples of challenges or gaps you’ve seen in current representations.
• Ideas for how standardized, computable representations could make your work easier or more effective.

Your input will help us identify priority areas and guide the development of shared solutions.