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Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting

Authors
  • Marshall, Charla1, 2, 3
  • Sturk-Andreaggi, Kimberly1, 2, 4
  • Ring, Joseph D.1, 2
  • Dür, Arne
  • Parson, Walther3, 5
  • 1 (J.D.R.)
  • 2 SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA
  • 3 Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
  • 4 Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
  • 5 Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
Type
Published Article
Journal
Genes
Publisher
MDPI AG
Publication Date
Sep 28, 2020
Volume
11
Issue
10
Identifiers
DOI: 10.3390/genes11101140
PMID: 32998193
PMCID: PMC7599696
Source
PubMed Central
Keywords
License
Green

Abstract

Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.

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