SIngle cell level Genotyping Using scRna Data (SIGURD)

Briefings in Bioinformatics, vol. 25

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 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 8

1. Martin Graßhoff Aachen Institute for Computational Genomics

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, RWTH Aachen University , Pauwelsstr. 30, 52074 Aachen, NRW ,

2. Milena Kalmer Aachen Department of Hematology, Oncology

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD) , Düsseldorf ,

   Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

3. Nicolas Chatain Aachen Department of Hematology, Oncology

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD) , Düsseldorf ,

   Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

4. Kim Kricheldorf Aachen Department of Hematology, Oncology

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD) , Düsseldorf ,

   Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

5. Angela Maurer Aachen Department of Hematology, Oncology

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD) , Düsseldorf ,

   Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

6. Ralf Weiskirchen Aachen Institute of Molecular Pathobiochemistry Experimental Gene Therapy and Clinical Chemistry

   RWTH Aachen University

   Affiliation as printed

   Institute of Molecular Pathobiochemistry , Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), , Pauwelstr 30, 52074 Aachen, NRW ,

7. Steffen Koschmieder corresponding Aachen Department of Hematology, Oncology

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD) , Düsseldorf ,

   Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

   RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,

8. Ivan G. Costa corresponding Aachen Institute for Computational Genomics

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, RWTH Aachen University , Pauwelsstr. 30, 52074 Aachen, NRW ,