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CLISGen: A Comprehensive Resource of SNP Genotypes for Human Cell Lines
Matteo Marchesin1, Davide Dalfovo2, Alessandro Romanel2
1Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy; University of Padova, Padova, Italy.
Journal of Molecular Biology
|February 8, 2026
Summary
CLISGen simplifies selecting cancer cell lines with specific Single Nucleotide Polymorphism (SNP) genotypes. This database aids functional genomics research by providing easy access to SNP data for over 1,000 cancer cell lines.
Area of Science:
- Genomics
- Cancer Research
- Bioinformatics
Background:
- Selecting cell lines with specific Single Nucleotide Polymorphism (SNP) genotypes is a significant challenge in functional genomics.
- This process often demands advanced bioinformatics expertise, hindering research progress.
Purpose of the Study:
- To develop CLISGen (Cell Lines SNP Genotypes), a user-friendly database and web application.
- To simplify and accelerate the selection of cancer cell lines based on SNP genotypes.
Main Methods:
- Integrated and harmonized SNP genotype data from Whole-Genome, Whole-Exome, and RNA sequencing for over 1,000 cancer cell lines.
- Enriched the dataset with copy number alterations and genetic ancestry information.
- Developed a web application for searching variants, genes, or genomic regions with filtering by tissue type and data quality.
Main Results:
- CLISGen provides intuitive graphical and tabular outputs for SNP genotype data.
- The platform facilitates efficient searching and filtering of cancer cell line genetic information.
- Successfully created a comprehensive resource for over 1,000 cancer cell lines.
Conclusions:
- CLISGen effectively addresses the bottleneck in selecting cell models for functional genomics.
- The database empowers researchers to efficiently identify cell lines for studying genotype-phenotype relationships in cancer.
- CLISGen is a valuable, freely accessible resource for the cancer research community.
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