1. F:\sarah\fri_MV

2. Multivariate Linkage and Association Sarah Medland and Manuel Ferreira -with heavy borrowing from Kate Morley and Frühling Rijsdijk

3. MV analyses can address Questions of common aetiology Same gene (snp) Co-incidental covariation due to LD between two different genes Co-variation due to shared social/environmental risk factors Aust. Albatross

4. MV analyses can address Questions of common aetiology Same gene (snp) Co-incidental covariation due to LD between two different genes Co-variation due to shared social/environmental risk factors Pleiotropy occurs when a single gene influences multiple phenotypic traits. Bilby

5. Studying multiple phenotypes… Run multiple univariate analyses on correlated traits Bandicoot

7. Studying multiple phenotypes… Run multiple univariate analyses Correct for multiple testing… Bonferroni  Correction for equivalent number of independent variables Doesn’t really address the idea of common aetiology Blue ringed octopus

8. Studying multiple phenotypes… Run multiple univariate analyses Try and determine if the coincident linkage/association is statistically unlikely Box jellyfish

9. Studying multiple phenotypes… Run multiple univariate analyses Try and determine if the coincident linkage/association is statistically unlikely Simulate/Permute data and assess how often this group of traits reaches this pattern of sig. by chance Brown Snake

10. Studying multiple phenotypes… Study a number of proxies  Cockatoo

11. Studying multiple phenotypes… Make a composite phenotype  Cuscus

12. Studying multiple phenotypes… Make a factor score combine both factor level and trait- specific effects latent factor effects are inherently pleiotropic residual effects are not assumes factor loadings are constant across genome Cuscus (again)

13. Alternative… Explicitly model the covariation between traits Traits may be correlated due to shared genetic factors (A) or shared environmental factors (C or E) ADHD E1E1 E2E2 A1A1 A2A2 a 11 2 IQ rGrG Q1Q1 Q2Q2 1 1111 1 1 rErE q 11 2 a 22 2 q 22 2 e 11 2 e 22 2 Dingo

14. Explicitly model the covariation between traits… Directly assess pleiotropy Increased power Esp. when the pattern of QTL effects is different from the background covariation ie positive r but gene effects are in opposite directions Reduced multiple testing Drop Bear

15. Multivariate analysis… In the context of linkage analysis when we have family data 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 Echidna

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. Within-Twin Covariances (Q) Q1Q1 q 11 q 21 1 Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +q 11 2 +e 11 2 Phenotype 2 a 11 a 21 +q 11 q 21 +e 11 e 21 a 22 2 +a 21 2 +q 21 2 +e 22 2 + e 21 2 Twin 1 Phenotype 1 Twin 1 Phenotype 2

23. Within-Twin Covariances (E) Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +q 11 2 +e 11 2 Phenotype 2 a 11 a 21 +q 11 q 21 +e 11 e 21 a 22 2 +a 21 2 +q 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

24. 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

25. 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

26. 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

27. 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

28. 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 1/0.5(a 22 2 +a 21 2 )+c 22 2 +c 21 2 Twin 1 Twin 2

29. Cross-Twin Covariances (Q) Twin 1 Phenotype 1 Twin 1 Phenotype 2 Q1Q1 q 11 q 21 1 Twin 2 Phenotype 1 Twin 2 Phenotype 2 Q1Q1 q 11 q 21 1 π Phenotype 1Phenotype 2 Phenotype 1 1/0.5a 11 2 +πq 11 2 Phenotype 2 1/0.5a 11 a 21 + π q 11 q 21 1/0.5(a 22 2 +a 21 2 )+ π q 21 2 Twin 1 Twin 2

30. Predicted Model Phenotype 1Phenotype 2Phenotype 1Phenotype 2 Phenotype 1 a 11 2 +q 11 2 +e 11 2 Phenotype 2 a 11 a 21 +q 11 q 21 +e 11 e 21 a 22 2 +a 21 2 +q 21 2 + e 22 2 +e 21 2 Phenotype 1 1/.5a 11 2 + π q 11 2 a 11 2 +q 11 2 +e 11 2 Phenotype 2 1/.5a 11 a 21 + πq 11 q 21 1/.5(a 22 2 +a 21 2 )+ π q 21 2 a 11 a 21 +q 11 q 21 +e 11 e 21 a 22 2 +a 21 2 +q 21 2 + e 22 2 +e 21 2 Twin 1 Twin 2 Within-twin covariance Cross-twin covariance

31. Running MV linkage analysis… Numerous programs Mx Solar Loki Merlin Repeated measures Computationally intensive Multiple boundary issues p-values difficult to obtain Emu (not e-moo)

32. MV association… Maximum likelihood – factor based approach Mx Canonical Correlation approach Plink Principal components approach F-bat Funnel Web Spider

33. Maximum likelihood approach Galah Unrelated individuals Shared variance due to a common factor Residual non-shared variance Family based data ACE type models

34. Common factor model Great white Phenotype 1 F1F1 E1E1 E2E2 f 11 f 21 e 11 e 22 1 1 Phenotype 2 Phenotype 3Phenotype 4 1 f 31 f 41 E3E3 e 33 1 E4E4 e 44 1

35. Factor level association Estimate a factor level beta Use the factor loadings as weights Add the uncorrected or grand mean 1 df Green Tree Frog

36. Factor level association Green Tree Frog Dot product see page 61 of the Mx manual

37. Factor level association Green Tree Frog Kronecker product see page 61 of the Mx manual

38. Variable specific association Estimate a separate beta for each trait Add the uncorrected or grand mean n df Kookaburra

39. Simulated data set 10 traits, Moderately correlated ~.4 1 snp, MAF.2 500 individuals Kingfisher

40. factorlevel.mx… dataset.ped Example Factor level association script - Boulder 2009 Sarah Medland Data NI=15 NGroups=1 Rec file=dataset.ped Labels fid iid a1 a2 genotype V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 Select genotype V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 ; Definition genotype ; Begin Matrices; F full 10 1 free ! factor R diag 10 10 free! residuals M full 10 1 free! grand means B full 1 1 free! association beta G full 1 1 ! genotype End Matrices; Numbat

41. factorlevel.mx… dataset.ped st.6 F 1 1 to F 10 1 st.4 R 1 1 to R 10 10 st 0 M 1 1 to M 10 1 sp G genotype Covariance (F*F')+(R*R') ; Means M + (B.G)@F ; Options multiple issat jiggle end drop B 1 1 1 end Perentie Monitor

42. variablespecific.mx… dataset.ped Example Factor level association script - Boulder 2009 Sarah Medland Data NI=15 NGroups=1 Rec file=dataset.ped Labels fid iid a1 a2 genotype V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 Select genotype V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 ; Definition genotype ; Begin Matrices; F full 10 1 free ! factor R diag 10 10 free! residuals M full 10 1 free! grand means B full 10 1 free! association beta G full 1 1 ! genotype End Matrices; Quoll

43. variablespecific.mx… dataset.ped st.6 F 1 1 to F 10 1 st.4 R 1 1 to R 10 10 st 0 M 1 1 to M 10 1 sp G genotype Covariance (F*F')+(R*R') ; Means M + (G@B).F ; Options multiple issat jiggle end drop B 1 1 1 to B 1 10 1 end Red back spider

44. Your task Run both FL and VS tests in Mx for the first data set Edit the data file name Calculate the p-value for the VS test using excel… Which variables are associated? What is the mean for variable 1 by genotype?

45. Results – factor level Difference Chi-squared >> 4.116 Difference d.f. >>>>>>>>> 1 Probability >>>>>>>>>>>> 0.042 Pademelon FBM 0.6080.1690.061 0.6700.068 0.6540.066 0.6140.062 0.6400.065 0.6590.066 0.6650.067 0.6040.061 0.6520.066 0.6590.066

46. Association with a factor score… Data set 1 Pigmy Possum

47. Results – variable specific Difference Chi-squared 46.361 Difference d.f. >>>> 10 Probability >>>>>>>> 1.2*10 -6 Rainbow Lorikeet FBM 0.6000.3880.139 0.6620.3930.155 0.6440.4600.176 0.6090.3170.115 0.6440.0750.029 0.6600.1310.051 0.675-0.042-0.017 0.615-0.087-0.032 0.6540.1070.042 0.668-0.019-0.008

48. Mean under different genotypes Salt water croc AA 0 AB 1 BB -0.2490.1390.527

49. Advantages to the ML approach Completely flexible Can be applied to any model Longitudinal models Simplex/Autoregressive processed Easy to add dominance etc Covariates Extends to family data Stone fish

50. Disadvantages Correction for multiple testing? FL & VS tests provide complementary information Inflation of type 1 error use a Bonferroni correction if you use both Taipan

51. Tassie Devil Tassie Tiger Tiger Snake Thorny Devil Tree Kangaroo Wombat Zebra finch