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Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light.

Philippine Garret1,2,3, Céline Bris4,5, Vincent Procaccio4,5

  • 1INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.

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|August 6, 2019
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Summary

This study developed a bioinformatics pipeline to analyze mitochondrial DNA (mtDNA) from exome sequencing data, identifying pathogenic variants in individuals with developmental and neurological disorders. This approach improves diagnostic yield without requiring new patient samples.

Keywords:
ES databioinformaticsmtDNApipeline

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Area of Science:

  • Genomics and Bioinformatics
  • Mitochondrial Genetics
  • Clinical Diagnostics

Background:

  • Exome sequencing (ES) generates vast amounts of data, including untargeted mitochondrial DNA (mtDNA) sequences.
  • Current diagnostic yields for mtDNA disorders can be improved by leveraging existing ES data.
  • Mitochondrial DNA variants are implicated in various developmental and neurological anomalies.

Purpose of the Study:

  • To develop and validate a bioinformatics strategy for deep analysis of mtDNA from ES data.
  • To increase the diagnostic yield for pathogenic mtDNA variants in a large cohort with developmental and/or neurological anomalies.
  • To integrate mtDNA variant detection into existing nuclear exome sequencing pipelines.

Main Methods:

  • A targeted bioinformatics pipeline was developed to assemble the mitochondrial genome from ES data.
  • mtDNA data were extracted from off-target sequences (indirect sequencing) in BAM files from 928 individuals.
  • Variants were filtered using database information, cohort frequencies, haplogroups, and predicted protein consequences.

Main Results:

  • Two homoplasmic pathogenic mtDNA variants (m.9035T>C and m.11778G>A) were identified in 0.2% of individuals.
  • The m.11778G>A variant was found in a patient with undiagnosed Leber's hereditary optic neuropathy (LHON).
  • Seven secondary findings (predisposing to deafness or LHON) were identified in 0.75% of the cohort.

Conclusions:

  • Integrating a targeted mtDNA analysis strategy into ES pipelines enhances diagnostic capabilities.
  • This approach effectively detects pathogenic mtDNA variants without additional patient sampling or targeted mtDNA sequencing.
  • The study highlights the value of re-analyzing existing ES data for improved diagnosis and research in mitochondrial disorders.