SIngle cell level Genotyping Using scRna Data (SIGURD)
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
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, which is an R-based pipeline for the clonal analysis of single-cell RNA-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. Availability Code and tutorial of SIGURD are available at GitHub https://github.com/CostaLab/sigurd . Contact ivan.costa@rwth-aachen.de , skoschmieder@ukaachen.de Supplementary Information Supplementary data are available online.
Authors 8
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Affiliation as printed
Institute for Computational Genomics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)
Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)
Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)
Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)
Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Ralf Weiskirchen Aachen Institute of Molecular Pathobiochemistry Experimental Gene Therapy and Clinical Chemistry
Affiliation as printed
Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)
Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Pauwelstr 30, 52074 Aachen, NRW, Germany
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Affiliation as printed
Institute for Computational Genomics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, NRW, Germany
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