Copy-scAT

Copy-scAT infers copy number variants (CNVs) from single-cell chromatin accessibility and epigenomic data to distinguish malignant from nonmalignant cells and enable analysis of subclonal chromatin dynamics in cancer.

Key Features:

• Implementation: Implemented as an R package for analysis of single-cell epigenomic data.
• CNV inference: Infers copy number variants (CNVs) from single-cell chromatin accessibility and epigenomic profiles.
• Malignancy deconvolution: Uses inferred CNVs to distinguish malignant cells from nonmalignant cells in clinical tumor specimens.
• Subclonal analysis: Enables identification and analysis of subclonal chromatin accessibility dynamics.
• Genotype–phenotype association: Associates genetic subclones with chromatin accessibility patterns and molecular phenotypes such as stem-like or differentiated states.
• Tumor heterogeneity focus: Applicable to malignancies with high intratumoral heterogeneity, including glioblastoma.
• Microenvironment analysis: Facilitates exploration of interactions between cancer cells and the tumor microenvironment.

Scientific Applications:

• Malignant vs nonmalignant cell identification: Deconvolving malignant and nonmalignant populations in single-cell epigenomic datasets from clinical tumor specimens.
• Subclonal chromatin dynamics mapping: Mapping chromatin accessibility changes across genetic subclones within tumors.
• Linking CNVs to regulatory states: Investigating how copy number variants influence chromatin accessibility and regulatory programs.
• Characterizing molecular phenotypes: Relating genetic subclones to molecular phenotypes such as stem-like or differentiated states.
• Studying intratumoral heterogeneity: Analyses of heterogeneity in cancers with complex subclonal architectures, exemplified by glioblastoma.
• Examining tumor–microenvironment interactions: Exploring how cancer cell genetics and chromatin states relate to interactions with the tumor microenvironment.

Methodology:

Implemented in R and infers copy number variants (CNVs) from single-cell chromatin accessibility/epigenomic data to classify malignant versus nonmalignant cells and support subclonal analyses.