Next-generation diagnostics and disease-gene discovery with the Exomiser

Damian Smedley; Julius O.B. Jacobsen; Marten Jäger; Sebastian Köhler; Manuel Holtgrewe; Max Schubach; Enrico Siragusa; Tomasz Zemojtel; Orion J. Buske; Nicole L. Washington; William P. Bone; Melissa A. Haendel; Peter N. Robinson

doi:10.1038/nprot.2015.124

Next-generation diagnostics and disease-gene discovery with the Exomiser

Damian Smedley, Julius O.B. Jacobsen, Marten Jäger, Sebastian Köhler, Manuel Holtgrewe, Max Schubach, Enrico Siragusa, Tomasz Zemojtel, Orion J. Buske, Nicole L. Washington, William P. Bone, Melissa A. Haendel, Peter N. Robinson

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Abstract

Exomiser is an application that prioritizes genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser comprises a suite of algorithms for prioritizing exome sequences using random-walk analysis of protein interaction networks, clinical relevance and cross-species phenotype comparisons, as well as a wide range of other computational filters for variant frequency, predicted pathogenicity and pedigree analysis. In this protocol, we provide a detailed explanation of how to install Exomiser and use it to prioritize exome sequences in a number of scenarios. Exomiser requires ∼3 GB of RAM and roughly 15-90 s of computing time on a standard desktop computer to analyze a variant call format (VCF) file. Exomiser is freely available for academic use from http://www.sanger.ac.uk/science/tools/exomiser.

Original language	English (US)
Pages (from-to)	2004-2015
Number of pages	12
Journal	Nature protocols
Volume	10
Issue number	12
DOIs	https://doi.org/10.1038/nprot.2015.124
State	Published - Dec 1 2015

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

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abstract = "Exomiser is an application that prioritizes genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser comprises a suite of algorithms for prioritizing exome sequences using random-walk analysis of protein interaction networks, clinical relevance and cross-species phenotype comparisons, as well as a wide range of other computational filters for variant frequency, predicted pathogenicity and pedigree analysis. In this protocol, we provide a detailed explanation of how to install Exomiser and use it to prioritize exome sequences in a number of scenarios. Exomiser requires ∼3 GB of RAM and roughly 15-90 s of computing time on a standard desktop computer to analyze a variant call format (VCF) file. Exomiser is freely available for academic use from http://www.sanger.ac.uk/science/tools/exomiser.",

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Next-generation diagnostics and disease-gene discovery with the Exomiser

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