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.



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Object Symbol
Species
Term
Qualifier
Evidence
With
Notes
Source
Original Reference(s)
CDK20Humanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs560019) (human)RGD 
Cdk20Ratalcohol dependence susceptibilityISORGD:1313116DNA:SNP:: (rs560019) (human)RGD 
Cdk20Mousealcohol dependence susceptibilityISORGD:1313116DNA:SNP:: (rs560019) (human)RGD 
PDE4BHumanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs1937443) (human)RGD 
Pde4bRatalcohol dependence susceptibilityISORGD:733361DNA:SNP:: (rs1937443) (human)RGD 
Pde4bMousealcohol dependence susceptibilityISORGD:733361DNA:SNP:: (rs1937443) (human)RGD 
TBX19Humanalcohol dependence susceptibilityIAGP DNA:SNP:: (rs1003502) (human)RGD 
Tbx19Ratalcohol dependence susceptibilityISORGD:1320875DNA:SNP:: (rs1003502) (human)RGD 
Tbx19Mousealcohol dependence susceptibilityISORGD:1320875DNA: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 susceptibilityISORGD:1320120DNA:SNP:: (rs1046655) (human)RGD 
Klhl5Mousecocaine dependence susceptibilityISORGD:1320120DNA:SNP:: (rs1046655) (human)RGD 
LRRC7Humancocaine dependence susceptibilityIAGP DNA:SNP: (rs1938584) (human)RGD 
Lrrc7Ratcocaine dependence susceptibilityISORGD:1349743DNA:SNP: (rs1938584) (human)RGD 
Lrrc7Mousecocaine dependence susceptibilityISORGD:1349743DNA:SNP: (rs1938584) (human)RGD 
TENM3Humancocaine dependence susceptibilityIAGP DNA:SNP:: (rs1514483) (human)RGD 
Tenm3Ratcocaine dependence susceptibilityISORGD:1315371DNA:SNP:: (rs1514483) (human)RGD 
Tenm3Mousecocaine dependence susceptibilityISORGD:1315371DNA:SNP:: (rs1514483) (human)RGD 
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1 to 19 of 19 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Notes
Source
Original 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 
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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)