Exome Sequencing for Epileptic Encephalopathy

Library preparation and capture for exome sequencing was performed at the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research using Agilent SureSelect Clinical Research Exome v2 (Agilent). Sequencing was performed on a HiSeqX (Illumina) to an average depth of coverage of 100× across captured regions. Alignments and variant calls were generated using SoftGenetics NextGene (version 2.4.1, SoftGenetics) to the February 2009 human genome assembly (GRCh37/hg19), and variant calls were restricted to coding regions and the canonical splice sites of an epileptic encephalopathy gene panel. Variants identified were then annotated using Alamut Batch (version 1.9, Interactive Biosoftware) and classified according to the American College of Medical Genetics (ACMG) criteria (Richards et al. 2015 (link)).

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Briere L.C., Walker M.A., High F.A., Cooper C., Rogers C.A., Callahan C.J., Ishimura R., Ichimura Y., Caruso P.A., Sharma N., Brokamp E., Koziura M.E., Mohammad S.S., Dale R.C., Riley L.G., Phillips J.A., Komatsu M, & Sweetser D.A. (2021). A description of novel variants and review of phenotypic spectrum in UBA5-related early epileptic encephalopathy. Cold Spring Harbor Molecular Case Studies, 7(3), a005827.

Publication 2021

Agilent SureSelect Clinical Research Exome v2 HiSeqX Alamut Batch

Encephalopathy Epileptic Exome Gene Human genome Library

Corresponding Organization :

Other organizations : Child Neurology Associates, Pediatrics and Genetics, Massachusetts General Hospital, Brigham and Women's Hospital, Niigata University, Vanderbilt University, Children's Hospital at Westmead, University of Sydney, Children's Medical Research Institute, Juntendo University

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Variable analysis

independent variables

Library preparation and capture for exome sequencing using Agilent SureSelect Clinical Research Exome v2
Sequencing on a HiSeqX (Illumina)

dependent variables

Average depth of coverage of 100× across captured regions
Alignments and variant calls generated using SoftGenetics NextGene (version 2.4.1, SoftGenetics) to the February 2009 human genome assembly (GRCh37/hg19)
Variant calls restricted to coding regions and the canonical splice sites of an epileptic encephalopathy gene panel
Variant annotation using Alamut Batch (version 1.9, Interactive Biosoftware) and classification according to the American College of Medical Genetics (ACMG) criteria

control variables

Performed at the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research

Annotations

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