Journal Article

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

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

2015

Overview

This protocol describes use of the Exomiser suite, a collection of algorithms that allow for prioritization of genes and variants from exome sequencing data for disease-gene discovery. 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 .

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/114/794 / 631/1647/48 / 631/208/212/2301 / 631/208/737 / Analytical Chemistry / Biological Techniques / Computational Biology/Bioinformatics / Diagnosis / Exome / Exome sequencing / Genes / Genetic disorders / Genetic screening / Genetic Testing - methods / Health aspects / High-Throughput Nucleotide Sequencing - methods / Humans / Identification and classification / Life Sciences / Methods / Microarrays / Organic Chemistry / Pathogens / protocol / Sequence Analysis, DNA - methods / Software