期刊
BMC BIOINFORMATICS
卷 23, 期 SUPPL 3, 页码 -出版社
BMC
DOI: 10.1186/s12859-022-04625-x
关键词
Single-cell RNA sequencing; Copy number variation; Single nucleotide variation; Entropy-based weighted integration
类别
资金
- National Heart, Lung, and Blood Institute
CAISC is an R package that integrates CNV and SNV data from scRNA-seq to identify clonal clusters with high accuracy. It allows for accurate examination of expression changes between subclones.
Background Although both copy number variations (CNVs) and single nucleotide variations (SNVs) detected by single-cell RNA sequencing (scRNA-seq) are used to study intratumor heterogeneity and detect clonal groups, a software that integrates these two types of data in the same cells is unavailable. Results We developed Clonal Architecture with Integration of SNV and CNV (CAISC), an R package for scRNA-seq data analysis that clusters single cells into distinct subclones by integrating CNV and SNV genotype matrices using an entropy weighted approach. The performance of CAISC was tested on simulation data and four real datasets, which confirmed its high accuracy in sub-clonal identification and assignment, including subclones which cannot be identified using one type of data alone. Furthermore, integration of SNV and CNV allowed for accurate examination of expression changes between subclones, as demonstrated by the results from trisomy 8 clones of the myelodysplastic syndromes (MDS) dataset. Conclusions CAISC is a powerful tool for integration of CNV and SNV data from scRNA-seq to identify clonal clusters with better accuracy than obtained from a single type of data. CAISC allows users to interactively examine clonal assignments.
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