SIngle cell level Genotyping Using scRna Data (SIGURD)
Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.
Authors
- Milena Kalmer
- Martin Graßhoff (ORCID: https://orcid.org/0000-0003-0951-4465)
- Kim Kricheldorf (ORCID: https://orcid.org/0000-0003-3102-2221)
- Ralf Weiskirchen (ORCID: https://orcid.org/0000-0003-3888-0931)
- Ivan G. Costa (ORCID: https://orcid.org/0000-0003-2890-8697)
- Angela Maurer
- Steffen Koschmieder
- Nicolas Chatain (ORCID: https://orcid.org/0000-0003-4485-3120)
Institutions
- Integrated Oncology (United States) (US)
- RWTH Aachen University (DE)
Publication Details
- Journal
- Briefings in Bioinformatics
- Published
- 2024-09-23
- DOI
- https://doi.org/10.1093/bib/bbae604
- Citations
- 2
- Primary Topic
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Type
- article
- Field-Weighted Citation Impact
- 0.88
Funders
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung
- RWTH Aachen University