ABSTRACT
In this proof-of-concept study, we developed a single cell method that identifies somatic alterations found in coding regions of mRNAs and integrates these mutation genotypes with their matching cell transcriptomes. We used nanopore adaptive sampling on single cell cDNA libraries, generated long read sequences from target gene transcripts and identified coding variants among individual cells. Short-read single cell transcriptomes characterized the cell types with mutations. We delineated CRISPR edits from a cancer cell line. From primary cancer samples, we targeted hundreds of cancer genes, identified somatic coding mutations and a gene rearrangement among individual tumor cells.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- AMP
- Adenosine monophosphate
- BED
- Browser Extensible Data format
- cAMP
- Cyclic adenosine monophosphate
- CRISPR
- Clustered Regularly Interspaced Short Palindromic Repeats
- gRNA
- guide RNA
- QC
- Quality Control
- scRNA-seq
- single-cell RNA sequencing
- SNV
- Single nucleotide variant
- TME
- Tumor microenvironment
- VAF
- Variant Allele Frequency
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.