RGD Reference Report - Substance dependence low-density whole genome association study in two distinct American populations. - Rat Genome Database

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Substance dependence low-density whole genome association study in two distinct American populations.

Authors: Yu, Yi  Kranzler, Henry R  Panhuysen, Carolien  Weiss, Roger D  Poling, James  Farrer, Lindsay A  Gelernter, Joel 
Citation: Yu Y, etal., Hum Genet. 2008 Jun;123(5):495-506. doi: 10.1007/s00439-008-0501-0. Epub 2008 Apr 26.
RGD ID: 401851917
Pubmed: PMID:18438686   (View Abstract at PubMed)
PMCID: PMC3428017   (View Article at PubMed Central)
DOI: DOI:10.1007/s00439-008-0501-0   (Journal Full-text)

Cocaine and opioid dependence are common, complex disorders with high heritability that commonly co-occur with other substance dependence disorders. Improved insight into the genetic basis of substance dependence would help elucidate its etiology and could inform its prevention and treatment. To generate new hypotheses about the genetics of substance dependence, we genotyped 5633 tagging single nucleotide polymorphism (SNP) markers in 1699 subjects from 339 African American (AA) families and 334 European American (EA) families ascertained through a sib pair meeting DSM-IV criteria for either cocaine or opioid dependence. The associations between genetic markers and five substance dependence traits (cocaine dependence, opioid dependence, cocaine-induced paranoia, alcohol dependence, and nicotine dependence) were assessed by family based association tests (FBAT). Results were ranked according to several criteria including statistical significance, concordance of results across population samples, and potential biological relevance of the implicated gene. The top-ranked result was an association of SNP rs1133503 in the MANEA gene with cocaine-induced paranoia (CIP). Our study provides an initial substance dependence trait-specific blueprint of associated regions for future candidate gene studies.



RGD Manual Disease Annotations    Click to see Annotation Detail View

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
CDK20Humanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs560019) (human)RGD 
Cdk20Ratalcohol dependence susceptibilityISOCDK20 (Homo sapiens)DNA:SNP:: (rs560019) (human)RGD 
Cdk20Mousealcohol dependence susceptibilityISOCDK20 (Homo sapiens)DNA:SNP:: (rs560019) (human)RGD 
PDE4BHumanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs1937443) (human)RGD 
Pde4bRatalcohol dependence susceptibilityISOPDE4B (Homo sapiens)DNA:SNP:: (rs1937443) (human)RGD 
Pde4bMousealcohol dependence susceptibilityISOPDE4B (Homo sapiens)DNA:SNP:: (rs1937443) (human)RGD 
TBX19Humanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs1003502) (human)RGD 
Tbx19Ratalcohol dependence susceptibilityISOTBX19 (Homo sapiens)DNA:SNP:: (rs1003502) (human)RGD 
Tbx19Mousealcohol dependence susceptibilityISOTBX19 (Homo sapiens)DNA:SNP:: (rs1003502) (human)RGD 
CCSER1Humancocaine dependence susceptibilityIAGP DNA:SNP:: (rs1381355) (human)RGD 
COL21A1Humancocaine dependence susceptibilityIAGP DNA:SNP:: (rs1925156) (human)RGD 
KLHL5Humancocaine dependence susceptibilityIAGP DNA:SNP:: (rs1046655) (human)RGD 
Klhl5Ratcocaine dependence susceptibilityISOKLHL5 (Homo sapiens)DNA:SNP:: (rs1046655) (human)RGD 
Klhl5Mousecocaine dependence susceptibilityISOKLHL5 (Homo sapiens)DNA:SNP:: (rs1046655) (human)RGD 
LRRC7Humancocaine dependence susceptibilityIAGP DNA:SNP: (rs1938584) (human)RGD 
Lrrc7Ratcocaine dependence susceptibilityISOLRRC7 (Homo sapiens)DNA:SNP: (rs1938584) (human)RGD 
Lrrc7Mousecocaine dependence susceptibilityISOLRRC7 (Homo sapiens)DNA:SNP: (rs1938584) (human)RGD 
TENM3Humancocaine dependence susceptibilityIAGP DNA:SNP:: (rs1514483) (human)RGD 
Tenm3Ratcocaine dependence susceptibilityISOTENM3 (Homo sapiens)DNA:SNP:: (rs1514483) (human)RGD 
Tenm3Mousecocaine dependence susceptibilityISOTENM3 (Homo sapiens)DNA:SNP:: (rs1514483) (human)RGD 
LCP1Humannicotine dependence susceptibilityIAGP DNA:SNP:: (rs1886040) (human)RGD 
Lcp1Ratnicotine dependence susceptibilityISOLCP1 (Homo sapiens)DNA:SNP:: (rs1886040) (human)RGD 
Lcp1Mousenicotine dependence susceptibilityISOLCP1 (Homo sapiens)DNA:SNP:: (rs1886040) (human)RGD 
RPTORHumannicotine dependence susceptibilityIAGP DNA:SNP:: (rs1062935) (human)RGD 
BMPERHumanopiate dependence susceptibilityIAGP DNA:SNP:: (rs731844) (human)RGD 
BmperMouseopiate dependence susceptibilityISOBMPER (Homo sapiens)DNA:SNP:: (rs731844) (human)RGD 
BmperRatopiate dependence susceptibilityISOBMPER (Homo sapiens)DNA:SNP:: (rs731844) (human)RGD 
C9Ratopiate dependence susceptibilityISOC9 (Homo sapiens)DNA:SNP:: (rs476569) (human)RGD 
C9Humanopiate dependence susceptibilityIAGP DNA:SNP:: (rs476569) (human)RGD 
C9Mouseopiate dependence susceptibilityISOC9 (Homo sapiens)DNA:SNP:: (rs476569) (human)RGD 
NAV3Humanopiate dependence susceptibilityIAGP DNA:SNP:: (rs770124) (human)RGD 
Nav3Ratopiate dependence susceptibilityISONAV3 (Homo sapiens)DNA:SNP:: (rs770124) (human)RGD 
Nav3Mouseopiate dependence susceptibilityISONAV3 (Homo sapiens)DNA:SNP:: (rs770124) (human)RGD 
TTC9Humanopiate dependence susceptibilityIAGP DNA:SNP:: (rs8688) (human)RGD 
Ttc9Mouseopiate dependence susceptibilityISOTTC9 (Homo sapiens)DNA:SNP:: (rs8688) (human)RGD 
Ttc9Ratopiate dependence susceptibilityISOTTC9 (Homo sapiens)DNA:SNP:: (rs8688) (human)RGD 
DNAH8HumanParanoid Disorders susceptibilityIAGP associated with cocaine dependence and DNA:SNP:: (rs1738240) (human)RGD 
Dnah8RatParanoid Disorders susceptibilityISODNAH8 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs1738240) (human)RGD 
Dnah8MouseParanoid Disorders susceptibilityISODNAH8 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs1738240) (human)RGD 
ICE2HumanParanoid Disorders susceptibilityIAGP associated with cocaine dependence and DNA:SNP:: (rs936013) (human)RGD 
Ice2RatParanoid Disorders susceptibilityISOICE2 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs936013) (human)RGD 
Ice2MouseParanoid Disorders susceptibilityISOICE2 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs936013) (human)RGD 
MANEAHumanParanoid Disorders susceptibilityIAGP associated with cocaine dependence and DNA:SNP:3'utr: (rs1133503) (human)RGD 
ManeaRatParanoid Disorders susceptibilityISOMANEA (Homo sapiens)associated with cocaine dependence and DNA:SNP:3'utr: (rs1133503) (human)RGD 
ManeaMouseParanoid Disorders susceptibilityISOMANEA (Homo sapiens)associated with cocaine dependence and DNA:SNP:3'utr: (rs1133503) (human)RGD 
TYK2HumanParanoid Disorders susceptibilityIAGP associated with cocaine dependence and DNA:SNP:: (rs280521) (human)RGD 
Tyk2MouseParanoid Disorders susceptibilityISOTYK2 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs280521) (human)RGD 
Tyk2RatParanoid Disorders susceptibilityISOTYK2 (Homo sapiens)associated with cocaine dependence and DNA:SNP:: (rs280521) (human)RGD 

Phenotype Annotations    Click to see Annotation Detail View

Manual Human Phenotype Annotations - RGD

Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
CDK20HumanAddictive alcohol use susceptibilityIAGP DNA:SNP:: (rs560019) (human)RGD 
PDE4BHumanAddictive alcohol use susceptibilityIAGP DNA:SNP:: (rs1937443) (human)RGD 
TBX19HumanAddictive alcohol use susceptibilityIAGP DNA:SNP:: (rs1003502) (human)RGD 
CCSER1HumanAddictive cocaine use susceptibilityIAGP DNA:SNP:: (rs1381355) (human)RGD 
COL21A1HumanAddictive cocaine use susceptibilityIAGP DNA:SNP:: (rs1925156) (human)RGD 
KLHL5HumanAddictive cocaine use susceptibilityIAGP DNA:SNP:: (rs1046655) (human)RGD 
LRRC7HumanAddictive cocaine use susceptibilityIAGP DNA:SNP: (rs1938584) (human)RGD 
MANEAHumanAddictive cocaine use susceptibilityIAGP  RGD 
TENM3HumanAddictive cocaine use susceptibilityIAGP DNA:SNP:: (rs1514483) (human)RGD 
LCP1HumanAddictive nicotine use susceptibilityIAGP DNA:SNP:: (rs1886040) (human)RGD 
RPTORHumanAddictive nicotine use susceptibilityIAGP DNA:SNP:: (rs1062935) (human)RGD 
BMPERHumanAddictive opioid use susceptibilityIAGP DNA:SNP:: (rs731844) (human)RGD 
C9HumanAddictive opioid use susceptibilityIAGP DNA:SNP:: (rs476569) (human)RGD 
NAV3HumanAddictive opioid use susceptibilityIAGP DNA:SNP:: (rs770124) (human)RGD 
TTC9HumanAddictive opioid use susceptibilityIAGP DNA:SNP:: (rs8688) (human)RGD 
DNAH8HumanParanoia susceptibilityIAGP DNA:SNP:: (rs1738240) (human)RGD 
ICE2HumanParanoia susceptibilityIAGP DNA:SNP:: (rs936013) (human)RGD 
MANEAHumanParanoia susceptibilityIAGP DNA:SNP:3'utr: (rs1133503) (human)RGD 
TYK2HumanParanoia susceptibilityIAGP DNA:SNP:: (rs280521) (human)RGD 
Objects Annotated

Genes (Rattus norvegicus)
Bmper  (BMP-binding endothelial regulator)
C9  (complement C9)
Cdk20  (cyclin-dependent kinase 20)
Dnah8  (dynein, axonemal, heavy chain 8)
Ice2  (interactor of little elongation complex ELL subunit 2)
Klhl5  (kelch-like family member 5)
Lcp1  (lymphocyte cytosolic protein 1)
Lrrc7  (leucine rich repeat containing 7)
Manea  (mannosidase, endo-alpha)
Nav3  (neuron navigator 3)
Pde4b  (phosphodiesterase 4B)
Tbx19  (T-box transcription factor 19)
Tenm3  (teneurin transmembrane protein 3)
Ttc9  (tetratricopeptide repeat domain 9)
Tyk2  (tyrosine kinase 2)

Genes (Mus musculus)
Bmper  (BMP-binding endothelial regulator)
C9  (complement component 9)
Cdk20  (cyclin dependent kinase 20)
Dnah8  (dynein, axonemal, heavy chain 8)
Ice2  (interactor of little elongation complex ELL subunit 2)
Klhl5  (kelch-like 5)
Lcp1  (lymphocyte cytosolic protein 1)
Lrrc7  (leucine rich repeat containing 7)
Manea  (mannosidase, endo-alpha)
Nav3  (neuron navigator 3)
Pde4b  (phosphodiesterase 4B, cAMP specific)
Tbx19  (T-box 19)
Tenm3  (teneurin transmembrane protein 3)
Ttc9  (tetratricopeptide repeat domain 9)
Tyk2  (tyrosine kinase 2)

Genes (Homo sapiens)
BMPER  (BMP binding endothelial regulator)
C9  (complement C9)
CCSER1  (coiled-coil serine rich protein 1)
CDK20  (cyclin dependent kinase 20)
COL21A1  (collagen type XXI alpha 1 chain)
DNAH8  (dynein axonemal heavy chain 8)
ICE2  (interactor of little elongation complex ELL subunit 2)
KLHL5  (kelch like family member 5)
LCP1  (lymphocyte cytosolic protein 1)
LRRC7  (leucine rich repeat containing 7)
MANEA  (mannosidase endo-alpha)
NAV3  (neuron navigator 3)
PDE4B  (phosphodiesterase 4B)
RPTOR  (regulatory associated protein of MTOR complex 1)
TBX19  (T-box transcription factor 19)
TENM3  (teneurin transmembrane protein 3)
TTC9  (tetratricopeptide repeat domain 9)
TYK2  (tyrosine kinase 2)


Additional Information