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MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data.

Mingqiang Wang1,2, Wankun Deng1, David C Samuels3,4

  • 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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|June 28, 2023
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Summary

MitoTrace is a new R package for analyzing mitochondrial genetic variation in single-cell RNA sequencing data. It robustly recovers mitochondrial variants, addressing limitations in current tools for heteroplasmy analysis.

Keywords:
R packageheteroplasmylineage tracingmitochondrial genetic variationsingle-cell RNA sequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genetic variations in the mitochondrial genome are crucial for biological functions and disease.
  • Single-cell RNA sequencing (scRNAseq) is a powerful tool for cellular transcriptomics.
  • Mitochondrial variants can be inferred from scRNAseq, but dedicated analysis tools are lacking.

Purpose of the Study:

  • To introduce MitoTrace, an R package for analyzing mitochondrial genetic variation in bulk and scRNAseq data.
  • To address the limitations of current variant calling tools for mitochondrial heteroplasmies.
  • To enable robust investigation of the single-cell landscape of mitochondrial variants.

Main Methods:

  • Development of MitoTrace, an R package for mitochondrial variant analysis.
  • Application of MitoTrace to diverse publicly available scRNAseq datasets.
  • Validation of MitoTrace performance across different scRNAseq platforms.

Main Results:

  • MitoTrace successfully and robustly recovers genetic variants from scRNAseq data.
  • The package demonstrates applicability across various scRNAseq data types and platforms.
  • MitoTrace provides a user-friendly approach to mitochondrial variant investigation.

Conclusions:

  • MitoTrace is an effective tool for analyzing mitochondrial genetic variation in scRNAseq data.
  • The package overcomes challenges associated with calling mitochondrial heteroplasmies.
  • MitoTrace facilitates deeper insights into mitochondrial biology and disease at the single-cell level.