A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations

Motivation: Staining the human metaphase chromosomes reveals characteristic banding patterns known as cytogenetic bands or cytobands. Using technologies based on metaphase chromosomes, researchers have accumulated much knowledge about the correlations between human diseases and specific cytoband aberrations, indicating the presence of disease-associated genes in those bands. With the progress of human genome project and techniques such as fluorescent in situ hybridization, many genes have been assigned to the cytobands and annotated in public databases, making it possible to find all genes in the disease-related cytobands through database queries. However, finding genes in cytobands remains an imprecise process, partly due to the insufficiency of current methods for cytoband queries, especially for those based on cytogenetic annotations. Results: By transforming the cytoband annotations into numerical segments, a new query method is developed that is able to accurately define any cytogenetic ranges in human chromosomes. A query system (designated cytoband query sys CQS) is implemented using cytogenetic annotations in the public domain. Judged by a performance test, CQS executed as accurately as expected using cytogenetic annotations from NCBI Map Viewer. The new method is scalable and can be applied to genomes from other species.