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Fig. 1 | BMC Bioinformatics

Fig. 1

From: CAISC: A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

Fig. 1

Clonal Architecture with Integration of SNV and CNV (CAISC). Overview of the computational framework that integrates both SNV and CNV profiles for clonal identification from scRNA-seq data. scRNA-seq reads are aligned with STAR, mutations are identified with GATK, and the read counts were calculated to represent gene expression. DENDRO is used to calculate a distance matrix based on allele reads of mutations. Infercnv is used to convert gene expression level data to a CNV profile matrix and then to calculate a distance matrix between cells. These two distance matrices are integrated using an entropy weighted method. Finally, a clonal tree is generated using the integrated matrix to more accurately identify subclones and infer their evolutionary relationship. The interactive figure generated by interactiveComplexHeatmap allows for manual examination of inferred clones

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BMC Bioinformatics

ISSN: 1471-2105

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