Categorical DataUnivariate Genetic AnalysisPractical ExampleContingency TablesRaw Dataset usmdd.ordFrequency Data: usmdd?.ctfSaturated Model! Estimate thresholds & correlations – Saturated ! US MDD data – females contingency tables! Estimate thresholds & correlations – Saturated ! US MDD data – females raw ordinal data! Estimate thresholds & correlations – Saturated ! US MDD data – females frequency dataDat File: usmdd.datSubmodels: Equality of ThresholdsACE Model! Estimate variance components - ACED model ! US MDD data - females! Estimate variance components - ACED model ! US MDD data - females II! Estimate variance components - ACED model ! US MDD data - females IIISubmodelsGoodness-of-FitCategorical DataHGEN619 2005Univariate Genetic AnalysisSaturated ModelsFree thresholdsUnivariate ModelsVariances partitioned in a, c/d and eFree thresholds (or not)Practical ExampleDataset: VTRFF1 interviewMDD (DSM-IIIR)Adults: 18-60 yearsN individuals MZF (zyg=1): 1180DZF (zyg=2): 880Contingency TablesMZF DZF T2T1- + T2T1- +- 329 83 - 201 94+ 95 83 + 82 63-: unaffected +: affectedRaw Dataset usmdd.ord 1 0 0 2 0 0 1 0 0 2 0 0 1 0 0 2 0 0 1 0 0 2 0 1 1 0 0 2 0 1 1 0 1 2 0 1 1 0 1 2 1 0 1 1 0 2 1 0 1 1 0 2 1 0 1 1 0 2 1 0 1 1 1 2 1 0 1 1 1 2 1 1 1 1 1 2 1 1Frequency Data: usmdd?.ctfMZ0 0 3290 1 831 0 951 1 83DZ0 0 2010 1 941 0 821 1 63Saturated ModelT2T11cor11t1t2! Estimate thresholds & correlations – Saturated! US MDD data – females contingency tables#NGroups 2#define nvar2 2Title 1: MZ data Data NInput=2 CTable 2 2 329 83 95 83 Begin Matrices; T Full nvar2 1 Free X Stnd nvar2 nvar2 Free End Matrices; Start 1 T 1 1 - T nvar2 1 Threshold T; Correlation X; Option RSidualsEndTitle 2: DZ data Data NInput=2 CTable 2 2 201 94 82 63 Begin Matrices; T Full nvar2 1 Free X Stnd nvar2 nvar2 Free End Matrices; Start 1 T 1 1 - T nvar2 1 Threshold T; Correlation X; Option RSiduals Option Multiple IssatEndusmddsatct.mx! Estimate thresholds & correlations – Saturated! US MDD data – females raw ordinal data#NGroups 2#define nvar2 2Title 1: MZ dataData NInput=3 Ordinal File=usmdd.ord Labels zyg mdd1 mdd2Select if zyg=1Select mdd1 mdd2 ; Begin Matrices; T Full 1 nvar2 Free X Stnd nvar2 nvar2 Free End Matrices; Start 1 T 1 1 - T 1 nvar2 Threshold T; Correlation X; Options RSidualsEndTitle 2: DZ dataData NInput=3 Ordinal File=usmddmz.ord Labels zyg mdd1 mdd2Select if zyg=2Select mdd1 mdd2 ; Begin Matrices; T Full 1 nvar2 Free X Stnd nvar2 nvar2 Free End Matrices; Start 1 T 1 1 - T 1 nvar2 Threshold T; Correlation X; Options RSidualsEndusmddsatord.mx! Estimate thresholds & correlations – Saturated! US MDD data – females frequency data#NGroups 2#define nvar2 2Title 1: MZ data Data NInput=3 Ordinal File=usmddmz.ctf Labels mdd1 mdd2 frq Definition frq ; Begin Matrices; T Full 1 nvar2 Free X Stnd nvar2 nvar2 Free F Full 1 1 End Matrices; Start 1 T 1 1 - T 1 nvar2 Specify F frq Threshold T; Correlation X; Frequency F;EndTitle 2: DZ data Data NInput=3 Ordinal File=usmdddz.ctf Labels mdd1 mdd2 frq Definition frq ; Begin Matrices; T Full 1 nvar2 Free X Stnd nvar2 nvar2 Free F Full 1 1 End Matrices; Start 1 T 1 1 - T 1 nvar2 Specify F frq Threshold T; Correlation X; Frequency F;Endusmddsatfrq.mxDat File: usmdd.dat Data NInput=3 Rectangular File=usmdd.ord Labels zyg mdd1 mdd2Submodels: Equality of ThresholdsMZ (group 1) DZ (group 2) part1 t2 v1 cor v2 t3 t4 v3 cor v4Full 1 2 0 3 0 4 5 0 6 0 6II 1 1 0 3 0 4 4 0 6 0 4III 1 1 0 3 0 1 1 0 6 0 3ACE ModelT2AEA Ca ac eT11 111Ee1Cc11 or .51! Estimate variance components - ACED model! US MDD data - females#NGroups 4#define nvar 1#define nvar2 2Title 1: Model Parameters Calculation Begin Matrices; X Lower nvar nvar Free !a Y Lower nvar nvar !c Z Lower nvar nvar Free !e W Lower nvar nvar Free !d H Full 1 1 !0.5 Q Full 1 1 !0.25 End Matrices; Matrix H .5 Matrix Q .25 Label Row X add_gen Label Row Y com_env Label Row Z spec_env Label Row W dom_genBegin Algebra; A= X*X'; !a^2 C= Y*Y'; !c^2 E= Z*Z'; !e^2 D= W*W'; !d^2 End Algebra;Endusmddaces.mx! Estimate variance components - ACED model! US MDD data - females II Title 2: MZ data #include usmdd.dat Select if zyg =1 Select mdd1 mdd2 ; Begin Matrices =Group 1; T Full 1 nvar2 Free End Matrices; Thresholds T; Covariance A+C+E+D | A+C+D _ A+C+D | A+C+E+D; Option RSiduals;EndTitle 3: DZ data #include usmdd.dat Select if zyg =2 Select mdd1 mdd2 ; Begin Matrices =Group 1; T Full 1 nvar2 Free End Matrices; Thresholds T; Covariance A+C+E+D |H@A+C+Q@D _ H@A+C+Q@D|A+C+E+D; Option RSidualsEndusmddaces.mx! Estimate variance components - ACED model! US MDD data - females IIITitle 4: Constrain var=1 Constraint Begin Matrices =Group 1; I Iden 1 1 End Matrices; Start .5 all St 1 T 2 1 1-T 2 1 nvar2 St 1 T 3 1 1-T 3 1 nvar2 Begin Algebra; P=A|C|E|D; End Algebra; Constraint A+C+E+D=I;!ADE model Option NDecimals=4 Option Sat=2508.004,2054 Option MultipleEnd!AE model Drop W 1 1 1End!ACE model Free Y 1 1 1End!CE model Drop X 1 1 1End!E model Drop Y 1 1 1Endusmddaces.mxSubmodelsMatrix / ModelX (a) Y (c) Z (e) W (d) Cor NPMean NPNP DFSat 2 4 6+1*ADE Free Free Free 4 7 0AE Free Free Drop 4 6 1ACE Free Free Free 4 7 0CE Drop Free Free 4 6 1E Drop Free 4 5 2*1 constraint: A+C+D+E=1Goodness-of-Fit-2LL df2df p AICSatADE 0AE 1ACE 0CE 1E
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