SIngle cell level Genotyping Using scRna Data (SIGURD).

ABSTRACT:

Motivation

By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3' ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.

Results

Here, we propose

SUBMITTER: Grasshoff M 

PROVIDER: S-EPMC11574290 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature