Tissue and Sex-Specific Performance of a Cancer Driver Based Biomarker in rasH2-Tg Mice

Area of Science:

• Toxicology and Carcinogenesis
• Genomics and Bioinformatics
• Cancer Risk Assessment

Background:

• Predicting rodent tumor response and extrapolating to humans are critical unmet needs in cancer risk assessment.
• Quantifying cancer driver mutations (CDMs) and understanding clonal expansion are key to addressing these needs.

Purpose of the Study:

• To validate and refine the CarcSeq method for quantifying CDMs and assessing clonal expansion using the median absolute deviation (MAD) biomarker.
• To leverage sex-related differences in spontaneous lung tumorigenesis in rasH2-Tg mice to test the CarcSeq/MAD approach.

Main Methods:

• Developed CarcSeq, an error-corrected next-generation sequencing (NGS) approach integrating CDM quantitation.
• Utilized high-fidelity PCR, unique identifier tagging, pooled amplicon library construction, and single-strand consensus sequencing for error correction.
• Employed median absolute deviation (MAD) in mutant fraction as a biomarker for clonal expansion.

Main Results:

• Significantly higher MAD was observed in male rasH2-Tg mice compared to females, correlating with increased spontaneous lung tumorigenesis.
• Males exhibited more recurrent mutations and a higher proportion of potentially selectable mutations.
• Sex-specific median analysis and COSMIC-based driver classification improved MAD analysis accuracy.

Conclusions:

• The CarcSeq/MAD biomarker approach is validated for assessing clonal expansion in cancer risk assessment.
• Technical insights into best practices for evaluating clonal expansion using CDM measurements were provided.
• This method enhances the ability to predict tumor responses and improve rodent-to-human extrapolation.