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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
MitImpact: an exhaustive collection of pre-computed pathogenicity predictions of human mitochondrial non-synonymous
Stefano Castellana1, Judit Rónai, Tommaso Mazza
1IRCCS Casa Sollievo della Sofferenza, Istituto Mendel, Bioinformatics Unit. Viale Regina Margherita, 261. 00198, Roma, Italy.
Abstract:
Mitochondrial DNA carries a tiny, but fundamental portion of the eukaryotic genetic code. As its nuclear counterpart, it is susceptible to point mutations. Their level of pathogenicity has been assessed for the newly discovered mutations only, leaving some degree of uncertainty on the potential impact of the unknown mutations. Here we present Mitochondrial mutation Impact (MitImpact), a queryable lightweight web interface to a reasoned collection of structurally and evolutionary annotated pathogenicity predictions, obtained by assembling pre-computed with on-the-fly-computed sets of pathogenicity estimations, for all the possible mitochondrial missense variants. It presents itself as a resource for fast and reliable evaluation of gene-specific susceptibility of unknown and verified amino acid changes. MitImpact is freely available at http://bioinformatics.css-mendel.it/ (tools section). ©2014 Wiley Periodicals, Inc.
Insights
Mitochondrial DNA mutations can cause disease, but predicting their impact is challenging. MitImpact offers a web tool for assessing pathogenicity of all possible mitochondrial missense variants, aiding genetic research.
Area of Science:
- Genetics
- Bioinformatics
- Molecular Biology
Background:
- Mitochondrial DNA (mtDNA) mutations are implicated in various diseases.
- Assessing the pathogenicity of novel mtDNA variants is crucial but challenging.
- Current methods often focus only on known mutations, leaving unknown variants unassessed.
Purpose of the Study:
- To develop a comprehensive resource for predicting the pathogenicity of all possible mitochondrial missense variants.
- To provide a user-friendly web interface for rapid and reliable evaluation of mtDNA variant impact.
- To integrate pre-computed and on-the-fly pathogenicity estimations for enhanced accuracy.
Main Methods:
- Developed MitImpact, a queryable web interface.
- Integrated structurally and evolutionarily annotated pathogenicity predictions.
- Combined pre-computed and on-the-fly computed pathogenicity estimations for all possible mitochondrial missense variants.
Main Results:
- MitImpact provides pathogenicity predictions for all possible mitochondrial missense variants.
- The resource combines diverse computational approaches for robust estimations.
- It enables fast and reliable evaluation of both known and unknown amino acid changes.
Conclusions:
- MitImpact serves as a valuable tool for researchers studying mitochondrial genetics and diseases.
- It facilitates the assessment of novel mitochondrial variants, improving diagnostic capabilities.
- The freely available web interface promotes wider accessibility and application in genetic research.
