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Numt identification and removal with RtN!

August E Woerner1,2, Jennifer Churchill Cihlar1,2, Utpal Smart2

  • 1Department of Microbiology, Immunology and Genetics.

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|July 25, 2020
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Summary

Nuclear mitochondrial DNA segments (Numts) interfere with mitochondrial genome analysis. The Remove the Numts! (RtN!) tool accurately removes Numts and sequencing noise without affecting variant calling, improving mitochondrial genomics accuracy.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Accurate read mapping and variant calling are crucial for mitochondrial genomics assays.
  • Nuclear-encoded mitochondrial DNA segments (Numts) possess distinct genetic properties that complicate mitochondrial genome data interpretation.
  • The presence of Numts can lead to inaccurate variant calling in mitochondrial genome analyses.

Purpose of the Study:

  • To develop a computational method for identifying and removing Numts from sequencing data.
  • To ensure that the removal of Numts does not negatively impact the accuracy of mitochondrial variant calling.
  • To provide a tool that enhances the reliability of mitochondrial genomics studies.

Main Methods:

  • Developed the Remove the Numts! (RtN!) tool for read categorization in massively parallel sequencing data.
  • RtN! utilizes sequence similarity to a comprehensive database of mitochondrial genomes for read classification.
  • The method focuses on removing low-level sequencing noise and Numts.

Main Results:

  • RtN! effectively categorizes and removes Numts and sequencing noise from mitochondrial genome data.
  • The tool demonstrated superior performance compared to competing methods, which were shown to remove true variants.
  • RtN! preserves the integrity of true mitochondrial variants during the filtering process.

Conclusions:

  • RtN! is an effective tool for improving the accuracy of mitochondrial genomics by removing confounding Numts.
  • The method enhances the reliability of variant calling in mitochondrial DNA analysis.
  • RtN! offers a valuable solution for researchers working with mitochondrial sequencing data.