2. Lifetime Prevalences of Externalizing and Substance Use Disorders Among Twins from Same-Sex Pairs

10. 3-Stage Conditional Model,Contingent Causal Common Pathway

11. Proportions of Variance Best Fitting CCC Model TI RU ND TI RU FTND TI RU P 0%20%40%60%80%100% No significant sex differences in proportions of variance or causal paths, but sex differences allowed in thresholds, No significant shared environmental effects for TI, RU and ND AiArAdEiErEd.89.69.87.93 -.29.87.70

12. Genetic Epidemiology of Alcoholism Family Studies Adoption Studies –Denmark –Sweden Twin Studies –Virginia, Sweden, Australia, WW-II and Vietnam Era Veteran twin registries

13. Estimated Genetic Proportions of Variance in Risk for Substance Abuse/Dependence 0

14. Genetic Epidemiology of Substance Abuse How do genetic risk factors for drug abuse relate to risk for psychiatric disorders?

15. Genetic Factors Major Depression GADPhobia Alcohol Dep Drug Abuse or Dep A SP A C2 A C1.54.24.13.33.06.10.58.18.65.21.00.22.38.46 Adult Antisocial Behavior Conduct Disorder A SP.00 A SP.17.53.56.11.37

16. Genetic Epidemiology of Substance Abuse How well does personality capture the genetic risk factors for substance initiation?

17. Genetic Individual Environ Novelty Seeking Shared Environ 83% 0%17% Cannabis Use Genetic Individual Environ Shared Environ 25% 42% 5% 7% 3% 18% Results from Bivariate Twin Model for Overlap of Novelty Seeking and Cannabis Use among Males Adapted from Table 1, Agrawal et al (2004), Twin Research, 7, 72-81

18. Are the Genetic Risk Factors for Drug Abuse in Part Genes for Personality? Genetic correlation between Novelty seeking (NS) and –Cannabis use – Males +0.96, Females +0.19 –Cocaine use – Males +0.62, Female +0.30

19. Are the Genetic Risk Factors for Drug Use in Part Genes for Personality? Genetic correlation between Extraversion and –Cannabis use +0.42 –Cocaine use +0.36 Genetic correlation between Neuroticism and –Cannabis use +0.18 –Cocaine use +0.18

20. Genetic Epidemiology of Substance Abuse How do the genetic risk for different forms of substance abuse relate to each other?

22. Genetic Epidemiology of Substance Abuse Begin to consider mediational models Genes → Intermediate phenotype → Drug Use Or, how do genes contribute to well understood risk factors for drug use and abuse?

23. Study the Availability of Drugs Life history data collection 8-11yrs 12-14yrs 15-17yrs 18-21yrs 22-25yrs Measures of drug availability - Alcohol- Marijuana- Stimulants - Cigarettes- Cocaine

24. “When you were…how easy would it have been to get [substance] if you wanted to use (it / them)?” 0. Very easy 1. Somewhat easy 2. Somewhat difficult 3. Very difficult

25. Age0123 8-1121%17%22%41% 12-1429%27%23%21% 15-1752%31%11%6% 18-2189%9%2%<1% Item endorsement Alcohol

26. Age0123 8-112%4%6%88% 12-148%11%16%65% 15-1724%21%19%36% 18-2145%25%14%17% 22-2546%26%14%13% Item endorsement Marijuana

27. Age0123 8-11<1%1%2%96% 12-142% 9%88% 15-176%8%18%68% 18-2117% 21%46% 22-2521%18%23%39% Item endorsement Cocaine

28. Alcohol 8-11yrs12-14yrs 15-17yrs 18-21yrs 8-11yrs12-14yrs 15-17yrs 18-21yrs

29. Marijuana 8-11yrs12-14yrs15-17yrs18-21yrs22-25yrs 8-11yrs12-14yrs15-17yrs18-21yrs22-25yrs

30. Cocaine 8-11yrs12-14yrs15-17yrs18-21yrs22-25yrs 8-11yrs12-14yrs15-17yrs18-21yrs22-25yrs

31. N01 23 1. 8-11 Cigarettes (b42)1790 43.520.4 15.120.9 2. 12-14 Cigarettes (c42)1795 56.824.3 12.06.8 3. 15-17 Cigarettes (d42)1792 78.415.6 4.12.0

32. Unstandardized and standardized proportions of variance in CIGARETTE availability. Variance components include latent genetic and environmental effects attributable to intercept and slope factors in the full biometrical DCS model.

35. Other Key Intermediate Phenotype – Peer Group Deviance Genes can act to increase liability to drug use disorders through influencing selection into high risk environments. –Example here – deviance of peer group –Many studies show peer group deviance to be a powerful predictor of subsequent drug use.

36. Modeling Time and Development and “Outside the Skin” Pathways Measures of peer group deviance retrospectively reported by a life history method. ~750 male-male twin pairs from Virginia Twin Registry. Evaluate 4 ages. Use a latent biometrical growth curve model –Can look separately at “genetics” of mean levels at different ages and –“Genetics” of slope (or trajectory).

39. Genetics of the Trajectory of Change in Peer Group Deviance From Ages 8-22 a 2 = 0.43 c 2 = 0.22 e 2 = 0.35 So, not only is the mean levels of peer group deviance influenced by genetic factors, but so is the rate of change over time.

40. Prevalence And Heritability Of Regular Tobacco Use Three Birth Cohorts Of Men And Women In Sweden Prevalence Of Heritability

42. Linkage And Association Linkage – in families. Sweeps entire genome. Good for genes of moderate to large effect. Association – in populations. Examines only small distances. Can detect genes of relatively small effect. If a base pair equals 1 cm, the human genome equals 33,000 km – around 80% of the way around the world. A linkage peak for a complex trait is ~ 200 km and association is detectable over distances from 50-200 meters.

46. Irish Affected Sib-Pair Study of Alcohol Dependence Samples & Measures Probands ascertained Interview & DNA N=591 (M=364, F=227) Parents contacted Brief Interview & DNA N=213 (M=82, F=131) Affected siblings referred Interview & DNA N=610 (M=413, F=197) 733 sib pairs (sibship size: 2-8) Control Groups Screened n = 72 Semi-screened ~ 600 Prescott et al., Alc Clin Exp Res, 2005

47. Sample & Measures IASPSAD families with DNA and informative for linkage (N=511 sib pairs, 485 families) 4 cM genome scan - deCODE genetics (Iceland) 1081 markers x 1500 individuals (1,621,500) Outcomes used for linkage analysis AD: DSM-IV Alcohol dependence SX: DSM-IV AD symptom count (range 3-7)

48. Genome-wide LOD Scores for DSM-IV Alcohol Dependence Ch1 Ch13 Ch22

49. Genome-wide LOD Scores for DSM-IV Alcohol Dependence Symptoms Ch4

50. Chromosome 4 Linkage Results Peak LOD = 4.59 (p<.000002)

51. Chromosome 4 linkage in other studies Southwest Indians: AD – Long et al. 1998 U.S. Collaborative (COGA): # symptoms – Reich et al 1998; max drinks - Saccone et al., 2000; alc response - Schuckit et al., 2001; severity – Corbett et al, 2005 Mission Indians: severity - Ehlers et al., 2004

52. Chromosome 4 NPL LOD Scores for Symptom Dropping Analyses medical consequences lack of control restricted activities withdrawal failed to quit binging tolerance ADSX

53. ADH cluster (1a,1b,1c,4,5,6,7)

54. ADH Follow-Up Association Studies 27 SNP markers identified in 7 genes Unrelated Case-Control design Stage 1: 328 cases randomly selected from probands & affected sibs 328 screened population controls Single-marker analyses Haplotype analyses –Haploview, WHAP

55. ADH Marker information 24 markers genotyped in ADH gene –ADH5 (including 3 SNPs: RS896992 RS1154405 RS1154400) –ADH4 (including 4 SNPs: RS1042364 RS1984360 RS1126671 RS4699712) –ADH6 (including 3 SNPs: RS3857224 RS2187483 RS4699733) –ADH1A (including 2 SNPs: RS1229976 RS1229967) –ADH1B (including 3 SNPs: RS1042026 RS1789882 RS1353621) –ADH1C (including 3 SNPs: RS1614972 RS1662060 RS3133158) –ADH7 (including 6 SNPs: RS894369 RS284786 RS1154454 RS1154458 RS1154460 RS971074)

56. Block structures of ADH gene from Haploview Standard Color Scheme D' < 1D' = 1 LOD < 2whiteblue LOD >=2 shades of pink/red bright red

57. (No missing data, n=383)(All data, filter out genotype missing over 25%, n=644) Association results for single marker analyses p<.05 p<.10

58. All Subjects (n=644) Excluding cases with missing data (n=383) Carol: Block 3 here is the Block 4 in above table. Notice that in the sample including only non-missing data, LD map from Haploview doesn’t have the block of marker 19 & 20 Haplotype association results for each block

59. The role of GABA A in alcohol dependence Most of the genes encoding for GABAA receptor subunits are organized in clusters located on different chromosomes. Thus, GABRA2, GABRA4, GABRB1, and GABRG1, encoding α2, α4, β1 and γ1 are on chromosome 4p13-12 whereas GABRA5, GABRB3, and GABRG3 encoding for α5, β3 and γ3 are located on 15q11-13. The clustering may have functional significance as studies suggest that variations in GABA A receptor genes contribute to differences in risk for alcoholism.

60. Alcoholism and GABA A receptor genes on 4p13-12 Several studies have reported the potential association of GABA A receptors and alcohol dependence. Song et al (2003) performed a family based association study using the large COGA (Collaborative Study on the Genetics of Alcoholism) sample. A modest association (P<0.03) was observed with GABRB1 and AD using microsatellite markers. Variations in GABRA2 were shown to be highly associated with AD as well as the beta frequency of the electroencephalogram (Edenberg et al, 2004). A comparision of the high-risk and low-risk haplotype coding sequences showed no differences hence the effect was postulated to be mediated through gene regulation. Further work has revealed a complex pattern of alternative splicing and promoter use (Tian et al, 2005). Other studies include Covault et al (2004) who reported an allelic and haplotypic association with GABRA2 and AD. Lappalainen et al (2005) showed that GABRA2 may play a role in risk for AD in a Russian population.

61. LD Pattern - D’ Plot

62. Single marker results using Whap SNP rs #HapMap locationGABAA geneP-value 149757045962576GABRG10.836 194860945978314GABRG10.683 222102046019107GABRG10.947 139116846030701GABRG10.541 49043446108821GABRA20.0075 49706846166219GABRA20.0165 27987146221275GABRA20.0167 27985846230135GABRA20.0678 27984546245265GABRA20.0685 27982646249751GABRA20.226 27982746250244GABRA20.138 27982846250352GABRA20.255 27983646254612GABRA20.0304 205594346882821GABRA40.767 151213546889430GABRA40.724 228007246910712GABRA40.193 205594046913455GABRA40.413 98980847082323GABRB10.219 137249647123350GABRB10.000004 628447237761GABRB10.987 207092247321590GABRB10.375

63. Results of haplotype analysis using Whap GABRA2 GABRA2 & GABRB1 HAPLOTYPEFREQUENCYP-VALUE 1222122210.4850.0205 2111211120.4700.0556 2222122210.0190.142 1211211120.0150.411 1222211110.0110.184 HAPLOTYPEFREQUENCYP-VALUE 12221222110.3890.817 21112111210.3680.00352 21112111220.1090.0322 12221222120.1020.0000697 22221222110.0170.25 12112111210.0150.427

64. This study provides further evidence that GABRA2 receptor gene is associated with AD. Previous studies have shown that SNPs in the 3’ region of the α2 subunit are significantly associated with AD (Covault et al, 2004; Edenberg et al, 2004). This study replicates the earlier findings; SNP rs490434 which is localized to the 3’ region produced a P-value of 0.0075. However the most significantly associated SNP in the current study is localized to GABRB1. SNP rs1372496 gave a single marker significance (P-value = 0.000004) when analyzed for AD.

65. Association Studies of Smoking Initiation and Nicotine Dependence Unrelated subjects from two twin studies Subjects were classified into 3 groups based on the score of the Fagerstrom Tolerance Questionnaire –244 NonSmokers –215 Low-ND smokers (FTQ score 0-2) –229 High-ND smokers (FTQ score 7-11)

66. January 11, 2016Sam CHEN A Summary of Genes Studied GenechrfunctionSIND Epac12cAMP signal transduction pathway ±+ PTEN10regulate AKT/PKB pathway +++ Rhoa3Ras gene family, signal pathway +++± Ywhag7 signal transduction (mitosis and cellular proliferation) -- MAP3K22MAPK signaling pathway -- MAP3K46MAPK signaling pathway -- MAP1222MAPK signaling pathway ±± ARHGAP 152a potential regulator of Rac1 -+ GABAB29GABA B2 receptor -- OPRM16opioid mu receptor ++

67. January 11, 2016Sam CHEN PTEN: Single Marker Association Marker name GenotypeAllele SINDSIND P-value rs12342210.08980.24370.03110.7252 rs22999390.71650.89290.52790.7720 rs12342130.00070.08210.00020.0278 rs27353430.00360.39080.00280.2105 rs7018480.47490.08560.15030.1161

68. January 11, 2016Sam CHEN PTEN: Haplotype Association Marker Global p valueHaplotype Frequency (case:ctrl) Odds ratio Haplotype p value Smoking Initiation 1-30.00531-20.36:0.271.330.0017 3-50.00782-10.35:0.261.380.0006 1-3-50.04311-2-10.32:0.241.340.0037 1-2-3-40.03081-1-2-20.34:0.271.250.0167 2-3-4-50.06471-2-2-10.34:0.261.280.0105 Nicotine Dependence 3-50.05042-10.40:0.311.30.0058

69. January 11, 2016Sam CHEN Rhoa: Single Marker Association Allelic associationGenotype association MarkerSINDSIND rs67848200.043190.475280.108300.74069 rs21772680.100680.285900.233710.51899 rs28782980.003490.702040.000050.00070 rs9744950.263050.755730.119840.92688 rs34480.108570.556430.279220.80291

70. January 11, 2016Sam CHEN Rhoa: Haplotype Association (SI) MarkerHaplotypeCaseFreqControlFreqORChisqP value 1-3-41-1-2180.50.29268.80.1891.88.160.0043 2-1-169.40.11274.60.2050.713.380.0003 2-2-183.70.13616.20.04547.520.0061 Global:LRS28.89 DF6 P6.38E-05 MarkerHaplotypeCaseFreqControlFreqORChisqP value 1-3-4-51-1-2-2100.00.17129.70.0862.07.390.00657 2-1-1-162.50.10770.80.2050.512.760.00035 2-2-1-182.10.14014.60.0423.39.570.00198 Global:LRS33.08 DF8 P5.96E-05