CLISGen: A Comprehensive Resource of SNP Genotypes for Human Cell Lines

• CLISGen is a user-friendly database and web application that provides access to SNP genotypes for over 1,000 cancer cell lines. • Genotypes were obtained by integrating and harmonizing WGS, WXS, and RNA-seq data from the Cancer Cell Line Encyclopedia. • Genotype information is enriched with key contextual data, such as copy number status and genetic ancestry. • The resource significantly accelerates the selection of suitable cell models for functional cancer genomics studies. Selecting cell lines with specific Single Nucleotide Polymorphism (SNP) genotypes is a critical bottleneck in functional genomics, often requiring advanced bioinformatic skills. To address this, we developed CLISGen (Cell Lines SNP Genotypes), a database with a user-friendly web application that simplifies access to SNP genotypes in over 1,000 cancer cell lines from the Cancer Cell Line Encyclopedia. CLISGen integrates and harmonizes data from Whole-Genome, Whole-Exome, and RNA sequencing, enriching it with contextual information like copy number alterations and genetic ancestry. The platform allows users to search for specific variants or variants in specific genes or genomic regions and filter results by tissue type or data quality, providing intuitive graphical and tabular outputs. By eliminating a major experimental bottleneck, CLISGen offers researchers a powerful resource to efficiently select suitable cell models for studying the link between genetic variation and cancer. CLISGen is freely available at https://bcglab.cibio.unitn.it/clisgen .