seqCAT

seqCAT authenticates biological samples and cell lines using RNA sequencing (RNA-seq) variant calls to detect mutations in expressed transcripts and verify sample identity against known cell-specific mutational profiles.

Key Features:

• Authenticity Verification: Interrogates mutations in expressed transcripts and cross-references them with publicly available cell-specific mutational profiles to confirm sample identity.
• Mutation Detection and Analysis: Identifies mutations within RNA sequences from RNA-seq variant calls to reveal genetic variations that may influence experimental outcomes.
• Cell Line Authentication: Compares mutational profiles against established databases to authenticate cancer research cell lines and detect contamination or genetic drift.
• Data Integration and Comparison: Facilitates integration and comparison of RNA-seq data across experiments, platforms, and laboratories to consolidate mutational profiles.

Scientific Applications:

• Validation of Cell Line Identity: Authenticates cell lines used in transcriptome profiling to ensure accuracy and reliability of experimental results.
• Demonstrated on Colorectal Cancer Cell Lines: Applied to COLO205, DLD1, HCT15, HCT116, HKE3, HT29, and RKO, validating reported synonymous relationships (e.g., DLD1 and HCT15) and detecting KRAS-G13D in HKE3 consistent with KRAS dosage mutants.
• Reanalysis of Public RNA-seq Data: Revisits existing RNA-seq experiments in public repositories to verify the authenticity of previously published data.

Methodology:

Analyzes RNA-seq variant calling data to detect mutations in expressed transcripts and cross-references these mutations with publicly available or established cell-specific mutational profiles, serving as an alternative authentication approach when whole-genome sequencing is unavailable.