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SIngle cell level Genotyping Using scRna Data (SIGURD).

Martin Grasshoff1, Milena Kalmer2,3, Nicolas Chatain2,3

  • 1Institute for Computational Genomics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, NRW, Germany.

Briefings in Bioinformatics
|November 19, 2024
PubMed
Summary

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This summary is machine-generated.

This study introduces SIGURD, an R-based pipeline for single-cell RNA sequencing data analysis. SIGURD quantifies clones using both somatic and mitochondrial variants, enabling functional analysis of gene expression changes within detected clones.

Area of Science:

  • Genomics
  • Computational Biology
  • Cancer Research

Background:

  • Single-cell RNA sequencing (scRNA-seq) can assess somatic variants and clonality.
  • Sparsity and protocol bias in scRNA-seq limit somatic variant detection.
  • Mitochondrial variants offer an alternative for clone identification.

Purpose of the Study:

  • To develop a computational tool for combined somatic and mitochondrial variant analysis in scRNA-seq data.
  • To enable functional characterization of gene expression changes within identified clones.
  • To address limitations of existing genotyping tools.

Main Methods:

  • Development of SIGURD (SIngle cell level Genotyping Using scRna Data), an R-based pipeline.
  • Leveraging both somatic and mitochondrial variants for clone quantification.
Keywords:
clonalityleukemiamyeloproliferative neoplasmssingle-cell RNA-seqsingle-cell genotyping

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  • Integration of clonal detection with functional analyses.

    • Main Results:

    • SIGURD enables clone quantification using both somatic and mitochondrial variants.
    • The pipeline facilitates functional analysis, including clone-cell population association and differential gene expression.
    • Demonstrated utility of SIGURD on myeloproliferative neoplasm patient data.

    Conclusions:

    • SIGURD provides a comprehensive approach for clonal analysis of scRNA-seq data.
    • The tool enhances the characterization of cellular clones and their associated gene expression profiles.
    • SIGURD advances the study of clonal heterogeneity in diseases like myeloproliferative neoplasms.