GWAS: Mesial temporal lobe epilepsy with hippocampal sclerosis
Description:
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Mesial temporal lobe epilepsy with hippocampal sclerosis. The EFO term Mesial temporal lobe epilepsy with hippocampal sclerosis was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Epilepsy (generalized). The EFO term epilepsy was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Exomes were sequenced in parent-child autism trios to determine if de novo mutations are responsible for risk of developing ASD in families with no prior history.
Authors:
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
A voltage-gated sodium channel subtype that is predominantly expressed in the CENTRAL NERVOUS SYSTEM. Defects in the SCN1A gene which codes for the alpha subunit of this sodium channel are associated with DRAVET SYNDROME, generalized epilepsy with febrile seizures plus, type 2 (GEFS+2), and familial hemiplegic migraine type 3.
Generated by gene2mesh v. 1.1.1
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Febrile seizures (MMR vaccine-related). The EFO term MMR-related febrile seizures was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
B Feenstra, B Pasternak, F Geller, L Carstensen, T Wang, F Huang, JL Eitson, MV Hollegaard, H Svanström, M Vestergaard, DM Hougaard, JW Schoggins, LY Jan, M Melbye, A Hviid
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Febrile seizures (MMR vaccine-unrelated). The EFO term febrile seizures was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
B Feenstra, B Pasternak, F Geller, L Carstensen, T Wang, F Huang, JL Eitson, MV Hollegaard, H Svanström, M Vestergaard, DM Hougaard, JW Schoggins, LY Jan, M Melbye, A Hviid
Number of patients with pediatric epilepsies and mutations in 30 genes
Description:
A study with a group of 349 patients showing symptoms of pediatric epilepsy (less than 5 years old) were subjected to targeted re-sequencing. A 30-gene panel was used to find causative mutations, and the number of patients with at least one mutation. Variants were called that were found in the exonic regions and those confined to intronic locations or in the 5 or 3' UTR's were discarded.
Causative mutations in 30 genes were established, and the number of patients with mutations in these 30 genes were presented in this gene set. All gene symbols were sanity checked with HGNC.
Authors:
Elena Parrini, Carla Marini, Davide Mei, Anna Galuppi, Elena Cellini, Daniela Pucatti, Laura Chiti, Domenico Rutigliano, Claudia Bianchini, Simona Virdò, Dalila De Vita, Stefania Bigoni, Carmen Barba, Francesco Mari, Martino Montomoli, Tiziana Pisano, Anna Rosati, , Renzo Guerrini
The chromosome 1 region has peak markers with of LOD of 3.45 and 3.46 for Alcoholism gender age and constraint as D1S2878 (165403366) D1S196 (167604128). Arbitrary interval of 25 MBp on each side of the peak makers was uploaded.
Authors:
Hill SY, Shen S, Zezza N, Hoffman EK, Perlin M, Allan W
All genes from DisGeNet and OMIM with evidence for an association is Epilepsy, found using the query term "epilepsy," are aggregated into this list. A binary score of 1 was added to indicate list membership.
All genes from DisGeNet and OMIM with evidence for an association is Autism Spectrum Disorder, found using the query term "Autism Spectrum Disorders" are aggregated into this list. A binary score of 1 was added to indicate list membership.
Postmortem human brain tissue from the caudate nucleus region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Postmortem human brain tissue from the putamen region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Down regulated genes from NAc compared to CN from race matched individuals
Description:
RNA sequencing was carried out on two striatal brain regions, caudate nucleus (CN) of the dorsal striatum and nucleus accumbens (NAc) of the ventral striatum, that are heavily implicated in Cocaine Use Disorder (CUD). Tissues were excised from postmortem samples from men with CUD and matched control subjects. Samples obtained from NAc from non-Hispanic white and black race individuals, were compared with those from CN from non-Hispanic white and black race individuals. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP399860; caudate nucleus UBERON:0001873 and nucleus accumbens UBERON:0001882.
Authors:
Philipp Mews, Ashley M Cunningham, Joseph Scarpa, Aarthi Ramakrishnan, Emily M Hicks, Sarah Bolnick, Susanna Garamszegi, Li Shen, Deborah C Mash, Eric J Nestler
Down regulated genes from nucleus accumbens (NAc) compared to caudate nucleus (CN), in race matched CUD diagnosed individuals
Description:
RNA sequencing was carried out on two striatal brain regions, caudate nucleus (CN) of the dorsal striatum and nucleus accumbens (NAc) of the ventral striatum, that are heavily implicated in Cocaine Use Disorder (CUD). Tissues were excised from postmortem samples from men with CUD and matched control subjects. Samples from NAc compared to CN in CUD diagnosed non-Hispanic white and black race individuals. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP399860; nucleus accumbens UBERON:0001882, caudate nucleus UBERON:0001873.
Authors:
Philipp Mews, Ashley M Cunningham, Joseph Scarpa, Aarthi Ramakrishnan, Emily M Hicks, Sarah Bolnick, Susanna Garamszegi, Li Shen, Deborah C Mash, Eric J Nestler
Down regulated genes from NAc with CUD in black race individuals compared to CN controls in white race individuals
Description:
RNA sequencing was carried out on two striatal brain regions, caudate nucleus (CN) of the dorsal striatum and nucleus accumbens (NAc) of the ventral striatum, that are heavily implicated in Cocaine Use Disorder (CUD). Tissues were excised from postmortem samples from men with CUD and matched control subjects. Samples from NAc from black race individuals with a CUD diagnosis, were to compared to CN from non-Hispanic white race control individuals. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP399860; nucleus accumbens UBERON:0001882, caudate nucleus UBERON:0001873.
Authors:
Philipp Mews, Ashley M Cunningham, Joseph Scarpa, Aarthi Ramakrishnan, Emily M Hicks, Sarah Bolnick, Susanna Garamszegi, Li Shen, Deborah C Mash, Eric J Nestler
Differentially expressed genes from RPE compared to Normal Retina
Description:
Transcriptome profiling from macular retina and RPE/choroid samples from 27 unrelated eye tissue donors, was performed using RNA-sequencing. Human donor eye collection were obtained from Utah Lions Eye Bank within a 6-hour post-mortem interval and donors aged 60-90 years. Sample types were Normal Retina, Intermediate AMD Retina, Neovascular AMD Retina, Normal macular retina pigment epithelium (RPE), Intermediate AMD RPE, and Neovascular AMD RPE. Age Related Macular Degeneration (AMD) phenotyping was determined using the Age-Related Eye Disease Study (AREDS) severity grading scale, where AREDS category 0/1 was considered normal, AREDS category 3 intermediate AMD, and AREDS category 4b neovascular AMD. Samples from Normal RPE were compared to Normal Retina, and are presented with fold change > 1.5 and and P < 0.05. This gene set was annotated from the Supplementry Table of BioRxiv pre-print paper ‘Patterns of gene expression and allele-specific expression vary among macular tissues and clinical stages of Age-related Macular Degeneration’ by Zhang et.al (2022) doi: https://doi.org/10.1101/2022.12.19.521092
RNA sequencing of a limited number of archived patients' specimens with extended opioid exposure or non-opioid exposure was performed. Immune infiltration and changes in the microenvironment were evaluated using CIBERSORT.
Authors:
Mamatha Garige, Sarah Poncet, Alexis Norris, Chao-Kai Chou, Wells W Wu, Rong-Fong Shen, Jacob W Greenberg, Louis Spencer Krane, Carole Sourbier
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC. Analyzed using GEO2R (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174409) separately for each brain region, comparing OUD and control samples.
Authors:
Xiangning Xue, Wei Zong, Jill R Glausier, Sam-Moon Kim, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Marianne L Seney, Ryan W Logan
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC. Analyzed using GEO2R (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174409) separately for each brain region, comparing OUD and control samples.
Authors:
Xiangning Xue, Wei Zong, Jill R Glausier, Sam-Moon Kim, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Marianne L Seney, Ryan W Logan
Postmortem tissue samples of the dorsolateral prefrontal cortex (DLPFC) from 153 deceased individuals (Mage = 35.4; 62% male; 77% European ancestry). Study groups included 72 brain samples from individuals who died of acute opioid intoxication, 53 psychiatric controls, and 28 normal controls. Whole transcriptome RNA-sequencing was used to generate exon counts, and differential expression was tested using limma-voom. Analyses were adjusted for relevant sociodemographic characteristics, technical covariates, and cryptic relatedness using quality surrogate variables. Weighted correlation network analysis and gene set enrichment analyses also were conducted.
Authors:
David W Sosnowski, Andrew E Jaffe, Ran Tao, Amy Deep-Soboslay, Chang Shu, Sarven Sabunciyan, Joel E Kleinman, Thomas M Hyde, Brion S Maher
Opioid controls_human_ dorsolateral prefrontal cortex and nucleus accumbens_coefficient
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
Opioid controls_human_ dorsolateral prefrontal cortex and nucleus accumbens_qvalue
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
Opioid use disorder_human_dorsolateral prefrontal cortex_coefficient
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
Opioid use disorder_human_nucleus accumbens_coefficient
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
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