EGAGenomicsWhole Genome Sequencinghttps://ega-archive.org/studies/EGAS00001007507EGAEGA study EGAS00001007507108 WGS of epileptic patients from the CENet cohortEGArestrictedepilepsy, Generalized seizure (finding), Epileptic seizures, Other forms of epilepsy (disorder), [X]Other epilepsy (disorder), Epilectic attack, Generalized fit, Seizure disorder (disorder), with intractable epilepsy, Epilepsy (disorder), Genome Sequencing, Epileptic fits, Seizure disorder, Other forms of epilepsy, unspecified, Epileptic disorder, Complete Genome, Client., EPILEP NEC W/O INTR EPIL, NOS, EPILEPSY NOS W INTR EPIL, Epileptic Seizure, Epileptic attack, Epileptic seizure (finding), seizure disorder, EP - Epilepsy, [X]Other epilepsy, EPILEPSY NEC W INTR EPIL, Other forms of epilepsy NOS, Other forms of epilepsy and recurrent seizures, Complete, Epilepsy, Whole Genome, Epileptic seizure, Complete Genome Sequencing, Epilepsy NOS (disorder), Epilepsy and recurrent seizures, Sequencing, EPILEP NOS W/O INTR EPIL, Epileptic fit, without mention of intractable epilepsy, Epilepsy NOS, Epileptic, Generalized seizure, Generalized convulsion, Patient, Clients, Whole, Generalised seizure, Generalised convulsion, Other forms of epilepsy NOS (disorder), EF - Epileptic fit, Generalised fit, Epileptic convulsionsF24O1_13, Disorders, chemical properties, Laboratory, [X]Other epilepsy (disorder), Epilectic attack, Seizure disorder (disorder), Biotin apo-protein ligase, Epilepsy (disorder), NINA C, partial epilepsy, biotin-acetyl-CoA carboxylase synthetase, ran, prevention, Long Term, high leaf temperature 1, KL receptor activity, unspecified, hierarchy, Occipital Lobe Epilepsy, systematics, Hominids, SCO5, SCO1, Software Engineering, Epileptic attack, Polymerase Chain, Akinetic Epilepsy, Research Activity, Gsfsow3, Laboratory Research, GPR168, Priorities, DmelCG9999, average, Other forms of epilepsy and recurrent seizures, thymus nucleic acid, Generalized Convulsive Epilepsy, Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase, Genomes, Epileptic seizure, Atonic Epilepsies, nucleic acid library preparation, HardwareType, composition, Abdominal Epilepsy, biotin:apocarboxylase ligase activity, W, Fast, paired, Benign Occipital Epilepsies, C1 4B, Generalized seizure, F24O1.13, Rhinencephalic Epilepsy, Bs, Amygdalo-Hippocampal Epilepsies, homozygous 2P16 deletion syndrome, ran-1, FAST, "Generalised epilepsy [Ambiguous]" EXACT [SNOMEDCT_2005_07_31:192989008], Anchored Polymerase Chain Reaction, preventive therapy, chemical characterization, acetyl CoA holocarboxylase synthetase activity, HRS, Epileptic seizures, Other forms of epilepsy (disorder), Gelastic, "Generalised epilepsy" EXACT [SNOMEDCT_2005_07_31:192994008], familial, Systematics, Longterm Effect, Research Priorities, FASTK, HSC, Auras, Awakening Epilepsy, not genetically inherited, xran, Software Tools, Nonconvulsive Generalized Seizure Disorder, DmelCG5125, PBT, Computer Applications, Epileptic disorder, Benign, Akinetic, Focal Seizure, [4)-3, Computer Applications Software, Sepharose C1, EPILEPSY NOS W INTR EPIL, desoxyribose nucleic acid, END, PCR, DRONINAC, Research and Development, pbt, CRAM, Software Applications, Gelastic Epilepsies, instrument, Source Software, content, Consciousness Preserved, Convulsive Generalized Seizure Disorder, whole genome, sodium hydrate, dRanGAP, polymerase chain reaction, Activities, Phenotypes, Applications, Epileptic, Focal Epilepsy, ds DNA, acetyl coenzyme A holocarboxylase synthetase activity, GPR140, 6.3.4.-, DNA, humans, "Generalized epilepsy" EXACT [NCI2004_11_17:C3021], Generalized Convulsive Epilepsies, krk1, Computer Software Applications, 6.3.4.9, Generalized Onset, Focal Seizure Disorder, lifespan, DNS, (Deoxyribonucleotide)n, Effects, Generalized fit, localisation-related epilepsy, Partial Epilepsies, Symptomatic Generalized, STK10, dran, Polymerase Chain Reactions, Seizure disorder, Other forms of epilepsy, ara24, Apes, Localization-Related Epilepsy, HRNBP2, Sd-RanGAP, Sd-RanGap, Deoxyribonucleic Acid, Homo, Subclinical Seizure, Nonconvulsive Epilepsy, Epileptic Seizure, Generalized Seizure Disorders, Awakening, NINAC, Ulip6, EP - Epilepsy, partial, Application, CG54125, Open Source Softwares, FOX2, NinaC, Occipital Epilepsies, focal epilepsy, Longterm, Software Application, Generalized Nonconvulsive, nucleic acid library construction, Open Source Software, Double Stranded, Pongidae, Nonconvulsive Generalized, Deoxyribonucleic acid, HNRBP2, Generalized Epilepsy, Long-Term, Seizure Disorder, Epileptic fit, Tonic, Computer Software Application, MRGF, Convulsive, Tools, Generalised convulsion, hrnbp2, fox2, Development and Research, (Deoxyribonucleotide)m, Anchored PCR, 2.2, generalized epilepsy, constitutitional genetic, chemical structure, biotin-acetyl coenzyme A carboxylase synthetase activity, ULIP-6, Generalized Epilepsies, Digestive, Epileptic convulsions, chemical composition, epilepsy, Lobe Epilepsy, epileptic syndrome, proto-oncogene c-Kit, biotin:apo-acetyl-CoA:carbon-dioxide ligase (ADP-forming) ligase (AMP-forming), CRMP-5, biotin--[acetyl-CoA carboxylase] synthetase activity, Generalized, DNAn+1, Simple Partial Epilepsies, ran10A, DRPLA, Localization-Related Epilepsies, compositionality, buffer, Homininus, Aura, Occipital Lobe, Tool, Uncinate Seizure, KIT ligand receptor activity, EPILEP NEC W/O INTR EPIL, Long Term Effects, chemical analysis, Epilepsies, high content screening, Benign Occipital, soda lye, Fxh, Generalized Convulsive, Subclinical, Library, Amygdalo-Hippocampal, XKrk1, Nonconvulsive, Epilepsy, library construction, prophylaxis, RanGap1, Childhood, fxh, CD117, Epilepsy and recurrent seizures, Cryptogenic Epilepsies, EPILEP NOS W/O INTR EPIL, Longterm Effects, Computer Programs, THC4, Generalized convulsion, Applications Softwares, C-Kit, control, Ssm, Convulsive Epilepsies, structure, Generalised seizure, Desoxyribonukleinsaeure, xkl-1, Aetznatron, Rhinencephalic, Ape, hereditary, Partial Epilepsy, formerly, PRED81, biotin--protein ligase activity, Activity, Digestive Epilepsies, determination, Sepharose C1 4B, Focal Seizure Disorders, instrument configuration, Dm NinaC, CG5125, Xkl-1, composed of, Classifications, Rhinencephalic Epilepsies, hierarchies, ranGap, ranGAP, Gsfsco1, B37, Generalized Onset Seizure Disorder, Occipital, rbm9a, rbm9b, AAF30287, Gsfsco5, prevention and control, Effect, Computer Program, Nonconvulsive Seizure Disorder, SOW3, RTA, Sepharose, hnrbp2, rangap, biotin-acetyl-CoA-carboxylase ligase activity, reference sample, Focal, entire life cycle, rbfox2-a, Simple, Open, SD, Seizure Disorders, Inverse Polymerase Chain Reaction, Computer Programs and Programming, free, rta, Biotin--[acetyl-CoA-carboxylase] ligase, genetic, preventive measures, Nina C, Hominin, Reaction, rbm9-b, Benign Focal Epilepsy, rbm9-a, Sd, Other forms of epilepsy NOS (disorder), Double-Stranded DNA, Research Priority, deoxyribonucleic acids, DRP-5., DNAn, Simple Partial Seizures, Natriumhydroxid, hydroxyde de sodium, Sl, Symptomatic, Long-Term Effects, Simple Partial, Amygdalo-Hippocampal Epilepsy, CT16120, Hominid, "Generalized epilepsy (disorder)" EXACT [SNOMEDCT_2005_07_31:19598007], Occipital Epilepsy, Benign Occipital Epilepsy, Generalized seizure (finding), CT28175, CYC, 4B, homozygous 2P21 deletion syndrome, Partial, Tr-kit, Abdominal Epilepsies, Epileptic fits, Double-Stranded, Fox-2, CG14670, Source Softwares, Digestive Epilepsy, Programs, (Deoxyribonucleotide)n+m, NOD, Taxonomies, Program, Partial Seizure Disorder, Gelastic Epilepsy, Computer Applications Softwares, kl1-A, NOS, Softwares, KIT, seizure disorder, HCS, Rasl2-8, tyrosine-protein kinase Kit, xrbm9, biotin holoenzyme synthetase activity, Atonic Epilepsy, NaOH, Nested Polymerase Chain Reaction, life, kit, chemical content, hcs, HiSeq 2500, Convulsive Epilepsy, Biotin--[methylcrotonoyl-CoA-carboxylase] ligase, without mention of intractable epilepsy, Epilepsy NOS, dJ106I20.3, epilepsy syndrome, Patient, partial epilepsies, Sepharose 4B, Focal Epilepsies, CG9999, inherited genetic, Childhood Benign Occipital Epilepsy, Generalized Seizure Disorder, taxonomy, with intractable epilepsy, SCF receptor activity, Computer, Inverse, Hominini, Localization-Related, aligned, epilepsies, Deoxyribonucleic acids, gDNA, hardware, Buffer, RanGAP, CRMP3-associated molecule, Childhood Benign Focal Epilepsy, Inverse PCR, Convulsive Seizure Disorder, Occipital Lobe Epilepsies, 6.3.4.11, scfr, 6.3.4.10, Cryptogenic, DmelCG1404, 6.3.4.15, UNC33-like phosphoprotein 6, Epileptic seizure (finding), SCFR, Other forms of epilepsy NOS, D12S755E, Fdc, Taxonomy, "Generalised epilepsy" EXACT [SNOMEDCT_2005_07_31:155038005], ninac, Research, entire lifespan, Partial Seizures, soude caustique, CG 5125, Uncinate, Seizures, Hominins, fox-2, "Generalised epilepsy" EXACT [SNOMEDCT_2005_07_31:155043003], ATP:Fas-activated serine/threonine protein phosphotransferase activity, Clients, Agarose, rbfox2, NEST:bs27h05, Long-Term Effect, EF - Epileptic fit, Generalized Nonconvulsive Epilepsy, Generalised fit, 6-An-alpha-L-Galp-(1->3)-beta-D-Galp-(1->]n, C21orf120, HHT1, Collapsin response mediator protein 5, Controlled, Applications Software, Open Source, Controlling, Computer Software, Edg, Biotin--[methylmalonyl-CoA-carboxytransferase] ligase, Atonic, Tonic Epilepsies, aligned to, Akinetic Epilepsies, Seizure, RBM9, Client, gsp1, OK/SW-cl.81, CG1404, TC4, tc4, Software Tool, Priority, rbm9, Generalized Nonconvulsive Seizure Disorder, Research Activities, caustic soda, DmelCG14670, Partial Seizure, CT42491, Subclinical Seizures, ds-DNA, Software, [X]Other epilepsy, EPILEPSY NEC W INTR EPIL, Anchored, c-KIT, l(1)G0075, Reactions, Nested, ARA24, Partial Seizure Disorders, Engineering, Tonic Epilepsy, Epilepsy NOS (disorder), Symptomatic Generalized Epilepsy, Panayiotopoulos Syndrome, acetyl-CoA carboxylase biotin holoenzyme synthetase activity, c-kit, Holocarboxylase synthetase, Crmp5, Abdominal, Cryptogenic Epilepsy, Gsp1, Nested PCR, assay, CRMP5, Uncinate Seizures, ORW1, Scl, RanfalseWhole genome sequencing of 108 epileptic patients from CENet cohortEpileptic patients have been sequenced as part of the CENet cohort which is composed of patients with Genetic Generalized Epilepsy (GGE) or Non-Acquired Focal Epilepsy (NAFE) collected in CHUM Research Center in Montreal. Patients were diagnosed by epileptologists. The clinical epilepsy phenotype was classified according to the current classification by the International League against Epilepsy (ILAE). 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’s 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 create a .cram file.2023-09-08 16:47:49EGAS000010075079606EGAD00001011301EGAC00001003396