A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest.

Abstract:

:Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in human medicine. Assuming that rare variants are more likely to be damaging, we designed a phylogeny-based prioritization workflow to obtain a reliable pool of candidate variants for further investigations. The prioritization workflow relies on an exhaustive functional annotation through the mtDNA extraction pipeline MToolBox and includes Macro Haplogroup Consensus Sequences to filter out fixed evolutionary variants and report rare or private variants, the nucleotide variability as reported in HmtDB and the disease score based on several predictors of pathogenicity for non-synonymous variants. Cutoffs for both the disease score as well as for the nucleotide variability index were established with the aim to discriminate sequence variants contributing to defective phenotypes. The workflow was validated on mitochondrial sequences from Leber's Hereditary Optic Neuropathy affected individuals, successfully identifying 23 variants including the majority of the known causative ones. The application of the prioritization workflow to cancer datasets allowed to trim down the number of candidate for subsequent functional analyses, unveiling among these a high percentage of somatic variants. Prioritization criteria were implemented in both standalone ( http://sourceforge.net/projects/mtoolbox/ ) and web version ( https://mseqdr.org/mtoolbox.php ) of MToolBox.

journal_name

Hum Genet

journal_title

Human genetics

authors

Santorsola M,Calabrese C,Girolimetti G,Diroma MA,Gasparre G,Attimonelli M

doi

10.1007/s00439-015-1615-9

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

121-36

issue

1

eissn

0340-6717

issn

1432-1203

pii

10.1007/s00439-015-1615-9

journal_volume

135

pub_type

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