Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2.

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• High-throughput DNA sequencing generates vast genomic data for cancer research.
• Accurate tumor ploidy and cellularity are crucial for advanced analyses like allele-specific copy-number and subclonality.
• Existing tools may lack comprehensive functionality for these higher-order analyses.

Purpose of the Study:

• To introduce CLONETv2, a versatile software tool for processing matched normal and tumor DNA sequencing data.
• To provide functions for calculating allele-specific copy number and identifying subclonal populations.
• To support advanced genomic analyses in cancer research and precision oncology.

Main Methods:

• CLONETv2 processes paired normal and tumor samples using patient-specific genotype data.
• It is independent of specific low-level bioinformatics tools.
• Offers high-level functions for allele-specific copy-number computation and subclonal population identification.

Main Results:

• CLONETv2 provides a complete set of functions for comprehensive analysis of matched tumor-normal sequencing data.
• Enables reliable estimation of tumor DNA ploidy and cellularity.
• Facilitates identification of subclonal tumor populations.

Conclusions:

• CLONETv2 is a valuable tool for cancer genomics, offering robust analysis of tumor DNA.
• Applicable to various sequencing data types (whole-genome, whole-exome, targeted) and sample sources (tissue, liquid biopsy).
• Enhances the capability for precision oncology by providing critical genomic insights.