Computational protocol: Novel motor phenotypes in patients with VRK1 mutations without pontocerebellar hypoplasia

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Protocol publication

[…] Prior to this study, the affected index patient in family 1 was prescreened for SMN1 mutations. Whole exome sequencing (WES) was performed by Axeq Technologies (Seoul, South Korea) using the Illumina (San Diego, CA) TrueSeq kit to generate sequencing data. Annotated WES data were examined for variants in genes selected for relevance to the phenotype. Preceding Sanger sequencing analysis of SETX, ALS2, SOD1, LMNA, MFN2, and TRPV4 did not identify any pathogenic mutations in the affected individual of family 2; subsequently WES was carried out at the University of Washington Genome Center. Data from VCF files were analyzed using the in-house Seave analysis pipeline (Kinghorn Centre for Clinical Genomics, Sydney, Australia) under homozygous and potentially compound heterozygote models. The effect of amino acid substitutions for sequence variants was assessed using the software SIFT and Polyphen2.Sanger sequencing was performed to confirm the mutations in the probands and for segregation analysis in family members. […]

Pipeline specifications

Software tools SIFT, PolyPhen
Databases Seave
Application WES analysis
Organisms Homo sapiens
Diseases Motor Neuron Disease