HumCFS

HumCFS curates human chromosomal fragile sites and annotates their genomic coordinates, cytobands, chemical inducers, gene and miRNA content to support analyses of chromosomal instability and disease-associated rearrangements.

Key Features:

• Fragile site catalog: HumCFS documents 125 human chromosomal fragile sites with precise chromosomal coordinates, cytoband locations, chemical inducers, and classification as common or rare based on induction frequency.
• Biological characterization: Common fragile sites are sensitive to replication stress and frequently undergo rearrangements in cancer, while rare fragile sites typically contain trinucleotide repeats.
• Gene mapping: Fragile site coordinates are mapped to protein-coding genes using Ensembl (GRCh38/hg38) to identify genes located within fragile regions.
• Gene-disease integration: Gene-disease associations are integrated from DisGeNET to link fragile-site genes to human diseases.
• miRNA mapping: Human miRNAs from miRBase are mapped to fragile site coordinates, indicating many miRNA genes reside within these regions.
• Analytical tools and formats: The resource incorporates JBrowse and BLAST for sequence and genomic analysis and provides data exports in text, GFF3, and BED formats compatible with the UCSC Genome Browser.

Scientific Applications:

• Chromosomal instability research: Enables investigation of genomic regions prone to breakage and their contribution to genomic rearrangements.
• Cancer genomics: Supports analysis of sites sensitive to replication stress and their rearrangements in tumors.
• Genetic disease and gene-disease association studies: Facilitates linking fragile-site genes and miRNAs to disease phenotypes via DisGeNET and miRBase mappings.

Methodology:

Coordinates for 125 fragile sites were curated and mapped to Ensembl (GRCh38/hg38) to identify protein-coding genes; human miRNAs from miRBase were mapped to fragile site coordinates; gene-disease associations were integrated from DisGeNET; JBrowse and BLAST were incorporated and data are provided in text, GFF3, and BED formats.