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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Next-generation diagnostics and disease-gene discovery with the Exomiser
Damian Smedley1, Julius O B Jacobsen1, Marten Jäger2,3
1Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK.
Nature Protocols
|November 13, 2015
Summary
Exomiser prioritizes genes and variants from next-generation sequencing data for disease-gene discovery. This application aids in diagnosing Mendelian diseases by analyzing exome sequences efficiently on standard computers.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Next-generation sequencing (NGS) generates vast amounts of data crucial for genetic research.
- Identifying causative genes for Mendelian diseases remains a significant challenge in diagnostics.
- Existing tools may lack comprehensive prioritization strategies for complex genetic data.
Purpose of the Study:
- To introduce Exomiser, a novel application for prioritizing genes and variants in NGS data.
- To detail the installation and application of Exomiser for exome sequence analysis.
- To facilitate novel disease-gene discovery and differential diagnostics of Mendelian diseases.
Main Methods:
- Utilizes random-walk analysis on protein interaction networks.
- Incorporates clinical relevance and cross-species phenotype comparisons.
- Applies computational filters including variant frequency, predicted pathogenicity, and pedigree analysis.
Main Results:
- Exomiser provides efficient prioritization of exome sequences.
- Analysis of a variant call format (VCF) file takes 15-90 seconds on a standard desktop.
- Requires approximately 3 GB of RAM for operation.
Conclusions:
- Exomiser offers a robust and efficient solution for genetic variant prioritization.
- The tool supports researchers in identifying disease-causing genes from NGS data.
- Exomiser is freely available for academic use, promoting wider adoption in genetic research.
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