Introduction to Multivariate Genetic Analysis Kate Morley and Frühling Rijsdijk 21st Twin and Family Methodology Workshop, March 2008.

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1 Introduction to Multivariate Genetic Analysis Kate Morley and Frühling Rijsdijk 21st Twin and Family Methodology Workshop, March 2008

2 Aim and Rationale Aim: to examine the source of factors that make traits correlate or co-vary Rationale:  Traits may be correlated due to shared genetic factors (A) or shared environmental factors (C or E)  Can use information on multiple traits from twin pairs to partition covariation into genetic and environmental components

3 Example 1 Why do traits correlate/covary? How can we explain the association?  Additive genetic factors (r G )  Shared environment (r C )  Non-shared environment (r E ) Kuntsi et al. (2004) Am J Med Genet B, 124:41 ADHD E1E1 E2E2 A1A1 A2A2  A11 2 IQ rGrG C1C1 C2C2 rCrC 1111 1 1 rErE  C11 2  A22 2  C22 2  E11 2  E22 2

4 Example 2 Associations between phenotypes over time  Does anxiety in childhood lead to depression in adolescence? How can we explain the association?  Additive genetic factors (a 21 )  Shared environment (c 21 )  Non-shared environment (e 21 )  How much is not explained by prior anxiety? Rice et al. (2004) BMC Psychiatry 4:43 Childhood anxiety A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Adolescent depression C1C1 C2C2 c 11 c 21 c 22 1 1

5 Sources of Information As an example: two traits measured in twin pairs Interested in:  Cross-trait covariance within individuals  Cross-trait covariance between twins  MZ:DZ ratio of cross-trait covariance between twins

6 Observed Covariance Matrix Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2

7 Observed Covariance Matrix Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance

8 Observed Covariance Matrix Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance

9 SEM: Cholesky Decomposition Twin 1 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 22 e 11 e 22 1 1 1 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 22 1 1

10 SEM: Cholesky Decomposition Twin 1 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1

11 SEM: Cholesky Decomposition Twin 1 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 Twin 2 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 2 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 1/0.5 1 1

12 Why Fit This Model? Covariance matrices must be positive definite If a matrix is positive definite, it can be decomposed into the product of a triangular matrix and its transpose:  A = X*X’ Many other multivariate models possible  Depends on data and hypotheses of interest

13 Cholesky Decomposition Path Tracing

14 Within-Twin Covariances (A) A1A1 A2A2 a 11 a 21 a 22 1 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

15 Within-Twin Covariances (A) A1A1 A2A2 a 11 a 21 a 22 1 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

16 Within-Twin Covariances (A) A1A1 A2A2 a 11 a 21 a 22 1 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

17 Within-Twin Covariances (A) A1A1 A2A2 a 11 a 21 a 22 1 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

18 Within-Twin Covariances (C) C1C1 C2C2 c 11 c 21 c 22 1 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

19 Within-Twin Covariances (E) Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 +e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Phenotype 1 E1E1 E2E2 e 11 e 21 e 22 1 1 Twin 1 Phenotype 2

20 Cross-Twin Covariances (A) Twin 1 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 1 Phenotype 2 Twin 2 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 2 Phenotype 2 1/0.5 Phenotype 1Phenotype 2 Phenotype 1 Phenotype 2 +c 11 c 21 +c 22 2 +c 21 2 Twin 1 Twin 2

21 Cross-Twin Covariances (A) Twin 1 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 1 Phenotype 2 Twin 2 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 2 Phenotype 2 1/0.5 Phenotype 1Phenotype 2 Phenotype 1 1/0.5a 11 2 + Phenotype 2 +c 11 c 21 +c 22 2 +c 21 2 Twin 1 Twin 2

22 Cross-Twin Covariances (A) Twin 1 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 1 Phenotype 2 Twin 2 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 2 Phenotype 2 1/0.5 Phenotype 1Phenotype 2 Phenotype 1 1/0.5a 11 2 +c 11 2 Phenotype 2 1/0.5a 11 a 21 +c 11 c 21 +c 22 2 +c 21 2 Twin 1 Twin 2

23 Cross-Twin Covariances (A) Twin 1 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 1 Phenotype 2 Twin 2 Phenotype 1 A1A1 A2A2 a 11 a 21 a 22 1 1 Twin 2 Phenotype 2 1/0.5 Phenotype 1Phenotype 2 Phenotype 1 1/0.5a 11 2 +c 11 2 Phenotype 2 1/0.5a 11 a 21 +c 11 c 21 1/0.5a 22 2 +1/0.5a 21 2 +c 22 2 +c 21 2 Twin 1 Twin 2

24 Cross-Twin Covariances (C) Twin 1 Phenotype 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 Twin 2 Phenotype 1 Twin 2 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 1 1 Phenotype 1Phenotype 2 Phenotype 1 1/0.5a 11 2 +c 11 2 Phenotype 2 1/0.5a 11 a 21 +c 11 c 21 1/0.5a 22 2 +1/0.5a 21 2 +c 22 2 +c 21 2 Twin 1 Twin 2

25 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +c 11 2 +e 11 2 Phenotype 2 a 11 a 21 +c 11 c 21 + e 11 e 21 a 22 2 +a 21 2 +c 22 2 + c 21 2 +e 22 2 +e 21 2 Phenotype 1 1/.5a 11 2 +c 11 2 a 11 2 +c 11 2 +e 11 2 Phenotype 2 1/.5a 11 a 21 + c 11 c 21 1/.5a 22 2 +1/.5 a 21 2 +c 22 2 +c 21 2 a 11 a 21 +c 11 c 21 + e 11 e 21 a 22 2 +a 21 2 +c 22 2 +c 21 2 +e 22 2 +e 21 2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance

26 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance

27 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance Variance of P1 and P2 the same across twins and zygosity groups

28 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance Covariance of P1 and P2 the same across twins and zygosity groups

29 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance within each trait differs by zygosity

30 Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 Variance P1 Phenotype 2 Covariance P1-P2 Variance P2 Phenotype 1 Within-trait P1 Cross-traitVariance P1 Phenotype 2 Cross-traitWithin-trait P2 Covariance P1-P2 Variance P2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance Cross-twin cross-trait covariance differs by zygosity

31 Example Covariance Matrix P1P2P1P2 P1 1 P2.301 P1 0.790.491 P2 0.500.590.291 P1P2P1P2 P1 1 P2 0.301 P1 0.390.251 P2 0.240.430.311 Twin 1 Twin 2 Twin 1 Twin 2 MZ DZ Within-twin covariance Cross-twin covariance

32 Example Covariance Matrix P1P2P1P2 P1 1 P2.301 P1 0.790.491 P2 0.500.590.291 P1P2P1P2 P1 1 P2 0.301 P1 0.390.251 P2 0.240.430.311 Twin 1 Twin 2 Twin 1 Twin 2 MZ DZ Within-twin covariance Cross-twin covariance

33 Example Covariance Matrix P1P2P1P2 P1 1 P2.301 P1 0.790.491 P2 0.500.590.291 P1P2P1P2 P1 1 P2 0.301 P1 0.390.251 P2 0.240.430.311 Twin 1 Twin 2 Twin 1 Twin 2 MZ DZ Within-twin covariance Cross-twin covariance

34 Example Covariance Matrix P1P2P1P2 P1 1 P2.301 P1 0.790.251 P2 0.240.590.291 P1P2P1P2 P1 1 P2 0.301 P1 0.390.251 P2 0.240.430.311 Twin 1 Twin 2 Twin 1 Twin 2 MZ DZ Within-twin covariance Cross-twin covariance

35 Example Covariance Matrix P1P2P1P2 P1 1 P2.301 P1 0.790.011 P2 0.010.590.291 P1P2P1P2 P1 1 P2 0.301 P1 0.390.011 P2 0.010.430.311 Twin 1 Twin 2 Twin 1 Twin 2 MZ DZ Within-twin covariance Cross-twin covariance

36 Summary Within-individual cross-trait covariance implies common aetiological influences Cross-twin cross-trait covariance implies common aetiological influences are familial Whether familial influences genetic or environmental shown by MZ:DZ ratio of cross-twin cross-trait covariances

37 Cholesky Decomposition Specification in Mx

38 Mx Parameter Matrices #define nvar 2 Begin Matrices; X lower nvar nvar free! Genetic coefficients Y lower nvar nvar free! C coefficients Z lower nvar nvar free! E coefficients G Full 1 nvar free! Means H Full 1 1 fix! 0.5 for DZ A covar End Matrices; Begin Algebra; A=X*X’;! A var/cov C=Y*Y’;! C var/cov E=Z*Z’; ! E var/cov P=A+C+E End Algebra;

39 Within-Twin Covariance P1 P2 A1A1 A2A2 a 11 a 21 a 22 1 1 Path Tracing:

40 Within-Twin Covariance P1 P2 A1A1 A2A2 a 11 a 21 a 22 1 1 Path Tracing: X Lower 2 x 2: P1 P2 A1A2

41 Within-Twin Covariance P1 P2 A1A1 A2A2 a 11 a 21 a 22 1 1 Path Tracing: X Lower 2 x 2: P1 P2 A1A2 a 11 a 21 a 22

42 Total Within-Twin Covar. Using matrix addition, the total within-twin covariance for the phenotypes is defined as:

43 Cross-Twin Covariance (DZ) P11 P21 A1A1 A2A2 a 11 a 21 a 22 1 1 P12 P22 A1A1 A2A2 a 11 a 21 a 22 1 1 0.5 Twin 1Twin 2

44 Cross-Twin Covariance (DZ) P11 P21 A1A1 A2A2 a 11 a 21 a 22 1 1 P12 P22 A1A1 A2A2 a 11 a 21 a 22 1 1 0.5 Twin 1Twin 2 Within-traits P11-P12 = 0.5a 11 2 P21-P22 = 0.5a 22 2 +0.5a 21 2

45 Cross-Twin Covariance (DZ) P11 P21 A1A1 A2A2 a 11 a 21 a 22 1 1 P12 P22 A1A1 A2A2 a 11 a 21 a 22 1 1 0.5 Twin 1Twin 2 Path Tracing: Within-traits P11-P12 = 0.5a 11 2 P21-P22 = 0.5a 22 2 +0.5a 21 2 Cross-traits P11-P22 = 0.5a 11 a 21 P21-P12 = 0.5a 21 a 11

46 Additive Genetic Cross-Twin Covariance (DZ) P11 P21 A1A1 A2A2 a 11 a 21 a 22 1 1 P12 P22 A1A1 A2A2 a 11 a 21 a 22 1 1 0.5 Twin 1Twin 2 Path Tracing: Within-traits P11-P12 = 0.5a 11 2 P21-P22 = 0.5a 22 2 +0.5a 21 2 Cross-traits P11-P22 = 0.5a 11 a 21 P21-P12 = 0.5a 21 a 11 N.B. in Mx  = @

47 Additive Genetic Cross-Twin Covariance (MZ) P11 P21 A1A1 A2A2 a 11 a 21 a 22 1 1 P12 P22 A1A1 A2A2 a 11 a 21 a 22 1 1 1 1 Twin 1Twin 2

48 Common Environment Cross- Twin Covariance P11 P21 C1C1 C2C2 c 11 c 21 c 22 1 1 P12 P22 C1C1 C2C2 c 11 c 21 c 22 1 1 1 1 Twin 1Twin 2

49 Covariance Model for Twin Pairs MZ:  CovarianceA+C+E | A+C_ A+C | A+C+E / DZ:  CovarianceA+C+E | H@A+C_ H@A+C | A+C+E / N.B. H Full 1 1 Fixed = 0.5

50 Obtaining Standardised Estimates

51 Correlated Factors Solution Phenotype 1 E1E1 E2E2 A1A1 A2A2  A11 2 Phenotype 2 rGrG C1C1 C2C2 rCrC 1111 1 1 rErE  C11 2  A22 2  C22 2  E11 2  E22 2 Each variable decomposed into genetic/environmental components Correlations across variables estimated Results from Cholesky can be converted to this model

52 Using matrix algebra notation: Covariance to Correlation

53 Genetic Correlations

54 Specification in Mx 1.Matrix function in Mx: R = \stnd(A); 2.R = \sqrt(I.A)˜ * A * \sqrt(I.A)˜; Where I is an identity matrix: and I.A =

55 Interpreting Results High genetic correlation = large overlap in genetic effects on the two phenotypes Does it mean that the phenotypic correlation between the traits is largely due to genetic effects?  No: the substantive importance of a particular r G depends the value of the correlation and the value of the  A 2 paths i.e. importance is also determined by the heritability of each phenotype

56 Example ADHD A1A1 A2A2  h P1 2 IQ rGrG 11  h P2 2 N.B.  h P1 2 =  A11 2 Proportion of r P due to additive genetic factors:

57 Standardised Results Begin algebra; K = A%P|C%P|E%P; End algebra; % is the Mx operator for element division Proportion of the phenotypic correlation due to genetic effects

58 Example Mx Output Matrix K:  Additive Genetic Component of ADHD = 63%, for IQ = 33%  % of covariance between ADHD and IQ due to A = 84% Matrix K Estimates [A%P|C%P|E%P] 1 2 3 4 5 6 1 0.6286 0.8360 0.0000 0.0000 0.3714 0.1640 2 0.8360 0.3338 0.0000 0.3666 0.1640 0.2996 [S=\STND(P)] [R=\STND(A)] 1 21 2 1 1.0000 -0.2865 1 1.0000 -0.2865 2 -0.2865 1.0000 2 -0.5248 1.0000 Phenotypic correlation Genetic correlation

59 Interpretation of Correlations Consider two traits with a phenotypic correlation of 0.40 : h 2 P1 = 0.7 and h 2 P2 = 0.6 with r G =.3 Correlation due to additive genetic effects = ? Proportion of phenotypic correlation attributable to additive genetic effects = ? h 2 P1 = 0.2 and h 2 P2 = 0.3 with r G = 0.8 Correlation due to additive genetic effects = ? Proportion of phenotypic correlation attributable to additive genetic effects = ? Correlation due to A: Divide by r P to find proportion of phenotypic correlation.

60 Interpretation of Correlations Consider two traits with a phenotypic correlation of 0.40 : h 2 P1 = 0.7 and h 2 P2 = 0.6 with r G =.3 Correlation due to additive genetic effects = 0.19 Proportion of phenotypic correlation attributable to additive genetic effects = 0.49 h 2 P1 = 0.2 and h 2 P2 = 0.3 with r G = 0.8 Correlation due to additive genetic effects = 0.20 Proportion of phenotypic correlation attributable to additive genetic effects = 0.49 Weakly heritable traits can still have a large portion of their correlation attributable to genetic effects.

61 More Variables… Twin 1 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 Twin 1 Phenotype 3 E3E3 e 33 e 31 e 32 C3C3 c 33 1 A3A3 a 33 c 32 a 31 c 31 a 32 1 1

62 More Variables… Twin 1 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 1 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 1/0.5 1 1 Twin 1 Phenotype 3 E3E3 e 33 e 31 e 32 C3C3 c 33 1 A3A3 a 33 c 32 a 31 c 31 a 32 1 1 Twin 2 Phenotype 1 A1A1 A2A2 E1E1 E2E2 a 11 a 21 a 22 e 11 e 21 e 22 1 1 1 1 Twin 2 Phenotype 2 C1C1 C2C2 c 11 c 21 c 22 1 1 Twin 2 Phenotype 3 E3E3 e 33 e 31 e 32 C3C3 c 33 1 A3A3 a 33 c 32 a 31 c 31 a 32 1 1 1/0.5 1

63 Mx Parameter Matrices #define nvar 3 Begin Matrices; X lower nvar nvar free! Genetic coefficients Y lower nvar nvar free! C coefficients Z lower nvar nvar free! E coefficients G Full 1 nvar free! Means H Full 1 1 fix! 0.5 for DZ A covar End Matrices; Begin Algebra; A=X*X’;! Gen var/cov C=Y*Y’;! C var/cov E=Z*Z’; ! E var/cov P=A+C+E End Algebra;

64 Expanded Matrices X Lower 3 x 3 Y Lower 3 x 3 Z Lower 3 x 3

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