Association of ultra-rare coding variants with genetic generalized epilepsy : A case–control whole exome sequencing study

Publisher Copyright: © 2022 The Authors. Epilepsia published by Wiley Periodicals LLC on behalf of International League Against Epilepsy.Objective: We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with familial and sporadic GGE. Methods: We performed a case–control whole exome sequencing study in unrelated individuals of European descent diagnosed with GGE (previously recruited and sequenced through multiple international collaborations) and ancestry-matched controls. The association of ultra-rare variants (URVs; in 18 834 protein-coding genes) with epilepsy was examined in 1928 individuals with GGE (vs. 8578 controls), then separately in 945 individuals with familial GGE (vs. 8626 controls), and finally in 1005 individuals with sporadic GGE (vs. 8621 controls). We additionally examined the association of URVs with familial and sporadic GGE in two gene sets important for inhibitory signaling (19 genes encoding γ-aminobutyric acid type A [GABAA] receptors, 113 genes representing the GABAergic pathway). Results: GABRG2 was associated with GGE (p = 1.8 × 10−5), approaching study-wide significance in familial GGE (p = 3.0 × 10−6), whereas no gene approached a significant association with sporadic GGE. Deleterious URVs in the most intolerant subgenic regions in genes encoding GABAA receptors were associated with familial GGE (odds ratio [OR] = 3.9, 95% confidence interval [CI] = 1.9–7.8, false discovery rate [FDR]-adjusted p =.0024), whereas their association with sporadic GGE had marginally lower odds (OR = 3.1, 95% CI = 1.3–6.7, FDR-adjusted p =.022). URVs in GABAergic pathway genes were associated with familial GGE (OR = 1.8, 95% CI = 1.3–2.5, FDR-adjusted p =.0024) but not with sporadic GGE (OR = 1.3, 95% CI =.9–1.9, FDR-adjusted p =.19). Significance: URVs in GABRG2 are likely an important risk factor for familial GGE. The association of gene sets of GABAergic signaling with familial GGE is more prominent than with sporadic GGE.Peer reviewe

Contaminomics

<p>Workflows for the detection and analysis of contaminant sequences in low biomass sRNA sequencing experiments, including preparation of figures and tables for a manuscript which is accessible here: https://www.biorxiv.org/content/early/2018/01/03/232975 . The same workflows are available in a git repository here: https://git.ufz.de/metaOmics/contaminomics/ .</p> <p> </p

Extension of protein topologies by ligand information: computation and visualization

<p>The Protein Topology Graph Library (PTGL) is a database of protein topologies that provides a web interface to compare and visualize protein folds based on the super-secondary structure. It uses a graph-based protein model related to earlier work by Koch et al.: the vertices of the protein graph represent the secondary structure elements<br>(SSEs) α-helix and β-sheet while the edges model contacts and spatial relations between these SSEs. Similarity between proteins is defined via common substructures in their protein graphs. In this work, the graph model has been extended to include ligand information and the new software VPLG that computes and visualizes the resulting protein graphs has been developed. VPLG reads and writes protein graphs in a custom text-based format, saves the resulting images in PNG or SVG format and comes with database support.</p

Overview genes involved in “Cell cycle process”, Ranked vs Nermal.

<p>Analysis of the overlap between our combined approach and Nermal for the GO biological process term “Cell cycle process” (GO:0022402). Top 150 of either our combined ranking or Nermal alone were analyzed for GO term “DNA repair” (GO:0006281) and these genes were discarded. The remaining lists (Ranking combination scheme: 89 genes and Nermal: 88 genes) were further compared. In total, 7 genes were found in common (<i>BACH1</i>, <i>NFE2L3</i>, <i>DDX11</i>, <i>CHEK2</i>, <i>MAPT</i>, <i>BUB1B</i>, <i>UBASH3A</i>). A combined list of the remaining genes (Ranking: 81 genes and Nermal: 82 genes; total 163 genes) was analyzed with the Genomatix Pathway System (GePS). The biological process term “Cell cycle process” was the most enriched (P-value: 4.83E−25). The relation between the different cell cycle proteins is depicted (red: candidates combined ranking scheme, blue: candidates Nermal).</p

Top 150 genes from the combined ranking.

<p>Top 150 genes from the combined ranking.</p

GO enrichment top 150 of Ranked, Nermal, and FuncNet.

<p>Number of genes observed with the GO terms “response to DNA damage stimulus” (GO:0006974) and “DNA repair” (GO:0006281) in the top 150 of our combined ranking approach “Ranked”, the literature mining tool “Nermal”, and the protein function prediction tool “FuncNet”. Number of genes observed, number of genes expected (P-value) for GO term “response to DNA damage stimulus” (GO:0006974): Ranked 71, 5 (5.50E−64); Nermal 65, 5 (7.10E−56); FuncNet 53, 5 (4.27E−42). GO term “DNA repair” (GO:0006281): Ranked 61, 4 (1.28E−60); Nermal 62, 3 (1.24E−62); FuncNet 47, 3 (1.54E−42).</p

Scoring scheme.

*<p>The FuncNet and Nermal scores were integrated and a new Fisher score was calculated that includes all FuncNet P-values as well as a P-value for Nermal. The “−1000” score is merely to clearly separate entries with Nermal/FuncNet scoring from those without. The maximum score possible with this scheme is 8.5.</p

The Fanconi anemia pathway.

<p>For further explanation see main text (newest FA member XRCC2 not shown).</p

Overview of the main intrinsic protein properties of sixteen FA proteins.

<p>NLS score: Nuclear Localization Signal score. pI: iso-electric point. Cellular localization: N = Nucleus; N/C = Nucleus and Cytoplasm. ^*These percentages have been calculated using RefSeq sequences as the orthologs assignment in EnsEMBL were incorrect. FANCE: EnsEMBL’s ortholog mouse protein incorrect; FANCE: NP_068741 (human: 100% identical with ENSP00000229769) and NP_001157291 (mouse). FANCF: no mouse ortholog available in EnsEMBL. FANCF: NP_073562.1 (human: 100% identical with ENSP00000330875) and NP_001108559.1 (mouse).</p

Distribution of haploinsufficiency probabilities (p(HI)).

<p>Distribution of haploinsufficiency probabilities (p(HI)) for the human genome (from Huang <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062017#pone.0062017-Huang1" target="_blank">[61]</a>). The mean p(HI) values for all human genes and 143 genes of our top 150 set are given as respectively, light blue and orange circles on the x-axis. p(HI)  = 1 means highly haploinsufficient, p(HI)  = 0 haplosufficient.</p