Whole genome and whole exome sequencing of epilaptic patients

In this project, we aim to identify genetic changes that predispose to epilepsy and those that predict the response to various anti-epileptic drugs. We sequenced whole genomes and whole exomes of epileptic individuals with different range of response to anti-epileptic drugs, and their relatives.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 2 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001004062	This dataset includes whole genome sequencing of 198 epileptic individuals. Libraries preparation and whole-genome sequencing: gDNA was cleaned up using ZR-96 DNA Clean & ConcentratorTM-5 Kit (Zymo) prior to being quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and its integrity assessed on agarose gels. Libraries were generated using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina) according to the manufacturer‚Äôs recommendations. Libraries were quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were denatured in 0.05N NaOH and diluted to 8pM using HT1 buffer. The clustering was done on a Illumina cBot and the flowcell was ran on a HiSeq 2500 for 2x125 cycles (paired-end mode) using v4 chemistry and following the manufacturer's instructions. A phiX library was used as a control and mixed with libraries at 0.01 level. Bioinformatics: The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.64. Program bcl2fastq v1.8.4 was used to demultiplex samples and generate fastq reads. The filtered reads were aligned to reference Homo_sapiens assembly b37. Each readset was aligned to creates a Binary Alignment Map file (.bam).	Illumina HiSeq 2500	198

Publications	Citations
Global characterization of copy number variants in epilepsy patients from whole genome sequencing. Monlong J, Girard SL, Meloche C, Cadieux-Dion M, Andrade DM, Lafreniere RG, Gravel M, Spiegelman D, Dionne-Laporte A, Boelman C, Hamdan FF, Michaud JL, Rouleau G, Minassian BA, Bourque G, Cossette P. PLoS Genet 14: 2018 e1007285	20
Unraveling the role of non-coding rare variants in epilepsy. Girard A, Moreau C, Michaud JL, Minassian B, Cossette P, Girard SL. PLoS One 18: 2023 e0291935	0