coverage of ∼30X. Reads were aligned using Isaac aligner (version 01.14) (Illumina Inc., Great Chesterford, UK) and mapped against the GRCh37 hg19 human assembly. Single nucleotide variants and insertions/deletions were identified using Isaac variant caller. Patients 4 and 5 were studied using a Haloplex panel (Agilent Technologies, Santa Clara, CA) of 95 epilepsy genes. Variants were called and annotated using the GATK10 toolkit and the ANNOVAR tool.11 Patient 7 was analyzed by WES using Nextera Rapid Capture Exome, Illumina NextSeq platform (Illumina Inc.) with an average coverage depth of 100–130X. An end-to-end in-house bioinformatics pipeline including base calling, primary filtering of low-quality reads and probable artefacts, and annotation of variants was applied.
