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 Psychosis (atypical). The EFO term psychosis 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:
T Kanazawa, M Ikeda, SJ Glatt, A Tsutsumi, H Kikuyama, Y Kawamura, N Nishida, T Miyagawa, R Hashimoto, M Takeda, T Sasaki, K Tokunaga, J Koh, N Iwata, H Yoneda
Genome-wide association study of stimulant dependence
Description:
A genome-wide association study for stimulant dependence was performed in a discovery cohort of African- (AA) and European-ancestry (EA) subjects ascertained for genetic studies of alcohol, opioid, and cocaine use disorders. The sample comprised individuals with DSM-IV stimulant dependence (393 EA cases, 5288 EA controls; 155 AA cases, 5603 AA controls). An independent cohort from the family-based Collaborative Study on the Genetics of Alcoholism (532 EA cases, 7635 EA controls; 53 AA cases, AA 3352 controls) was used for replication. One variant in SLC25A16 (rs2394476, p = 3.42 × 10-10, odds ratio [OR] = 3.70) was GWS in AAs. Four other loci showed suggestive evidence, including KCNA4 in AAs (rs11500237, p = 2.99 × 10-7, OR = 2.31) which encodes one of the potassium voltage-gated channel protein that has been linked to several other substance use disorders, and CPVL in the combined population groups (rs1176440, p = 3.05 × 10-7, OR = 1.35), whose expression was previously shown to be upregulated in the prefrontal cortex from users of cocaine, cannabis, and phencyclidine. Analysis of the top GWAS signals revealed a significant enrichment with nicotinic acetylcholine receptor genes (adjusted p = 0.04) and significant pleiotropy between stimulant dependence and alcohol dependence in EAs (padj = 3.6 × 10-3), an anxiety disorder in EAs (padj = 2.1 × 10-4), and ADHD in both AAs (padj = 3.0 × 10-33) and EAs (padj = 6.7 × 10-35).
Authors:
Jiayi Cox, Richard Sherva, Leah Wetherill, Tatiana Foroud, Howard J Edenberg, Henry R Kranzler, Joel Gelernter, Lindsay A Farrer
Data from GEO GSE194368 and analyzed using GEO2R, only top gene shown. Authors identified transcriptional adaptations of GR signaling in the amygdala of humans with OUD. Thus, GRs, their coregulators and downstream systems may represent viable therapeutic targets to treat the “stress side” of OUD.
Authors:
Stephanie A Carmack, Janaina C M Vendruscolo, M Adrienne McGinn, Jorge Miranda-Barrientos, Vez Repunte-Canonigo, Gabriel D Bosse, Daniele Mercatelli, Federico M Giorgi, Yu Fu, Anthony J Hinrich, Francine M Jodelka, Karen Ling, Robert O Messing, Randall T Peterson, Frank Rigo, Scott Edwards, Pietro P Sanna, Marisela Morales, Michelle L Hastings, George F Koob, Leandro F Vendruscolo
Genome-wide association studies are conducted of two human cohorts, one group demonstrating nicotine dependence and another successfully quitting smoking. Study shows that some genetic components associated with the ability to quit overlap while many do not overlap. To perform the study, DNA samples were obtained from NIH volunteers and the allelic frequencies of the samples were analyzed using Affymetrix array analysis. This gene set comprises 290 genes associated with nicotine dependence.
Authors:
Drgon T, Montoya I, Johnson C, Liu QR, Walther D, Hamer D, Uhl GR
Striatum Gene Expression Correlates for COCA_TIME_PCT_CHANGE measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The COCA_TIME_PCT_CHANGE measures Cocaine CPP - difference in percent test time spent relative to preconditioning under the domain Cocaine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
cocaine related behavior 7 (Cocrb7) spans 28.968906 - 78.968906 Mbp (NCBI Build 37) on Chr 6. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for cocaine related behavior on Chr6 at D6Mit183 (53.97 Mbp , Build 37)
Description:
cocaine related behavior spans 28.97 - 78.97 Mbp (NCBI Build 37) on Chr6. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for METH responses for body temperature on Chr6 at D6Ncvs34 (54.50 Mbp , Build 37)
Description:
METH responses for body temperature spans 29.50 - 79.50 Mbp (NCBI Build 37) on Chr6. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for ethanol induced locomotion on Chr6 at NA (64.65 Mbp , Build 37)
Description:
ethanol induced locomotion spans 39.65 - 89.65 Mbp (NCBI Build 37) on Chr6. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Hitzemann R, Demarest K, Koyner J, Cipp L, Patel N, Rasmussen E, McCaughran J Jr
QTL for METH responses for home cage activity on Chr6 at D6Nds3 (67.84 Mbp , Build 37)
Description:
METH responses for home cage activity spans 42.84 - 92.84 Mbp (NCBI Build 37) on Chr6. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for METH responses for body temperature on Chr6 at D6MIt16 (67.84 Mbp , Build 37)
Description:
METH responses for body temperature spans 42.84 - 92.84 Mbp (NCBI Build 37) on Chr6. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Genes associated with Homo sapiens that interact with the MeSH term 'entinostat' (C118739). Incorporates data from 11 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Oryctolagus cuniculus that interact with the MeSH term 'Ionomycin' (D015759). Incorporates data from 6 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine' (C516138). Incorporates data from 3 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'vorinostat' (C111237). Incorporates data from 13 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Mitoxantrone' (D008942). Incorporates data from 2 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'nickel sulfate' (C029938). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Copper Sulfate' (D019327). Incorporates data from 72 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Platichthys flesus that interact with the MeSH term 'pentabromodiphenyl ether' (C086401). Incorporates data from 4 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Oryzias latipes that interact with the MeSH term 'Ethinyl Estradiol' (D004997). Incorporates data from 13 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Cyclosporine' (D016572). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'sodium arsenite' (C017947). Incorporates data from 15 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Gadus morhua that interact with the MeSH term 'methylmercuric chloride' (C004925). Incorporates data from 4 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Oryctolagus cuniculus that interact with the MeSH term 'Lipopolysaccharides' (D008070). Incorporates data from 23 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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