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Univariate Twin Analysis. OpenMx Tc26 2012 Hermine Maes, Elizabeth Prom-Wormley, Nick Martin. Overall Questions to be Answered. Does a trait of interest cluster among related individuals? Can clustering be explained by genetic or environmental effects?

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Univariate twin analysis
Univariate Twin Analysis

  • OpenMx Tc26 2012

  • Hermine Maes, Elizabeth Prom-Wormley, Nick Martin


Overall questions to be answered
Overall Questions to be Answered

  • Does a trait of interest cluster among related individuals?

  • Can clustering be explained by genetic or environmental effects?

  • What is the best way to explain the degree to which genetic and environmental effects affect a trait?


Family twin study designs
Family & Twin Study Designs

  • Family Studies

  • Classical Twin Studies

  • Adoption Studies

  • Extended Twin Studies


The data

569 total MZ pairs

351 total DZ pairs

The Data

  • Australian Twin Register

  • 18-30 years old, males and females

  • Work from this session will focus on Body Mass Index (weight/height2) in females only

  • Sample size

    • MZF = 534 complete pairs (zyg = 1)

    • DZF = 328 complete pairs (zyg = 3)



Classical twin studies basic background
Classical Twin Studies Basic Background

  • The Classical Twin Study (CTS) uses MZ and DZ twins reared together

    • MZ twins share 100% of their genes

    • DZ twins share on average 50% of their genes

  • Expectation- Genetic factors are assumed to contribute to a phenotype when MZ twins are more similar than DZ twins


Classical twin study assumptions
Classical Twin StudyAssumptions

  • MZ twins are genetically identical

  • Equal Environments of MZ and DZ pairs


Basic data assumptions
Basic Data Assumptions

  • MZ and DZ twins are sampled from the same population, therefore we expect :-

    • Equal means/variances in Twin 1 and Twin 2

    • Equal means/variances in MZ and DZ twins

  • Further assumptions would need to be tested if we introduce male twins and opposite sex twin pairs


Old fashioned data checking
Old Fashioned” Data Checking

Nice, but how can we actually be sure that these means and variances are truly the same?


Univariate analysis a roadmap
Univariate AnalysisA Roadmap

  • 1- Use the data to test basic assumptions (equal means & variances for twin 1/twin 2 and MZ/DZ pairs)

    • Saturated Model

  • 2- Estimate contributions of genetic and environmental effects on the total variance of a phenotype

    • ACE or ADE Models

  • 3- Test ACE (ADE) submodels to identify and report significant genetic and environmental contributions

    • AE or CE or E Only Models

10



Saturated code deconstructed

mMZ1

mDZ1

mMZ2

mDZ2

Saturated Code Deconstructed

mean MZ = 1 x 2 matrix

mean DZ = 1 x 2 matrix


Saturated code deconstructed1

T1

T1

T2

T2

T1

T1

T2

T2

Saturated Code Deconstructed

covMZ = 2 x 2 matrix

covDZ = 2 x 2 matrix


Time to play with openmx please open the file twinsatcon r
Time to Play... with OpenMxPlease Openthe FiletwinSatCon.R


Estimated values
Estimated Values

  • 10 Total Parameters Estimated

mMZ1, mMZ2, vMZ1,vMZ2,cMZ21

mDZ1, mDZ2, vDZ1,vDZ2,cDZ21

  • Standardize covariance matrices for twin pair correlations (covMZ & covDZ)


Estimated values1
Estimated Values

  • 10 Total Parameters Estimated

mMZ1, mMZ2, vMZ1,vMZ2,cMZ21

mDZ1, mDZ2, vDZ1,vDZ2,cDZ21

  • Standardize covariance matrices for twin pair correlations (covMZ & covDZ)


Fitting nested models
Fitting Nested Models

  • Saturated Model

    • likelihood of data without any constraints

    • fitting as many means and (co)variances as possible

  • Equality of means & variances by twin order

    • test if mean of twin 1 = mean of twin 2

    • test if variance of twin 1 = variance of twin 2

  • Equality of means & variances by zygosity

    • test if mean of MZ = mean of DZ

    • test if variance of MZ = variance of DZ




Stats
Stats

No significant differences between saturated model

and models where means/variances/covariances

are equal by zygosity and between twins


Questions
Questions?

This is all great, but we still don’t understand the genetic and environmental contributions to BMI


Patterns of twin correlation
Patterns of Twin Correlation

???

rMZ > 2rDZ

Additive &

Dominance

DZ twins on average share 25% of dominance effects

rMZ = 2rDZ

Additive

DZ twins on average share 50% of additive

effects

rMZ = rDZ

Shared Environment

Additive & “Shared Environment”

A = 2(rMZ-rDZ)

C = 2rDZ - rMZ

E = 1- rMZ


Bmi twin correlations

A = 0.96

C = -0.20

E = 0.22

0.78

0.30

BMI Twin Correlations

A = 2(rMZ-rDZ)

C = 2rDZ - rMZ

E = 1- rMZ

ADE or ACE?


Univariate analysis a roadmap1
Univariate AnalysisA Roadmap

  • 1- Use the data to test basic assumptions inherent to standard ACE (ADE) models

    • Saturated Model

  • 2- Estimate contributions of genetic and environmental effects on the total variance of a phenotype

    • ADE or ACE Models

  • 3- Test ADE (ACE) submodels to identify and report significant genetic and environmental contributions

    • AE or E Only Models


Ade model a few considerations
ADE ModelA Few Considerations

  • Dominance refers to non-additive genetic effects resulting from interactions between alleles at the same locus

  • ADE models also include effects of interactions between different loci (epistasis)

  • In addition to sharing on average 50% of their DNA, DZ twins also share about 25% of effects due to dominance


Ade model deconstructed path coefficients
ADE Model Deconstructed Path Coefficients

covA <- mxAlgebra( expression=a %*% t(a), name="A" )

covD <- mxAlgebra( expression=d %*% t(d), name=“D" )

covE <- mxAlgebra( expression=e %*% t(e), name="E" )

1 x 1 matrix

1 x 1 matrix

1 x 1 matrix


Ade model deconstructed variance components
ADE Model DeconstructedVariance Components

*

1 x 1 matrix

*

1 x 1 matrix

*

1 x 1 matrix


Ade model deconstructed means covariances

expMean

expMean

ADE Model DeconstructedMeans & Covariances

expMean= 1 x 2 matrix

T1

T2

T1

T2

covMZ & covDZ= 2 x 2 matrix


Ade model deconstructed means covariances1
ADE Model DeconstructedMeans & Covariances

T1

T2

T1

T2

T1

T2

T1

T2


Ade model deconstructed means covariances2
ADE Model DeconstructedMeans & Covariances

T1

T2

T1

T2

T1

T2

T1

T2


Ade model deconstructed
ADE Model Deconstructed

4 Parameters Estimated

ExpMean

Variance due to A

Variance due to D

Variance due to E


Univariate analysis a roadmap2
Univariate AnalysisA Roadmap

  • 1- Use the data to test basic assumptions inherent to standard ACE (ADE) models

    • Saturated Model

  • 2- Estimate contributions of genetic and environmental effects on the total variance of a phenotype

    • ADE or ACE Models

  • 3- Test ADE (ACE) submodels to identify and report significant genetic and environmental contributions

    • AE or E Only Models


Testing specific questions please open twinadecon r
Testing Specific Questions Please Open twinADEcon.R

  • ‘Full’ ADE Model

    • Comparison against Saturated

  • Nested Models

    • AE Model

      • test significance of D

    • E Model vs AE Model

      • test significance of A

    • E Model vs ADE Model

      • test combined significance of A & D


Ae model deconstructed

New Object

Containing

AE Model

Object containing

Full Model

The d

path will not be

estimated

Fixing the value of the c path to zero

AE Model Deconstructed

AeModel <- mxModel( AdeFit, name="AE" )

AeModel <- omxSetParameters( AeModel,

labels=“d11", free=FALSE, values=0)

AeFit <- mxRun(AeModel)





Univariate analysis a roadmap3
Univariate AnalysisA Roadmap

  • 1- Use the data to test basic assumptions inherent to standard ACE (ADE) models

    • Saturated Model

  • 2- Estimate contributions of genetic and environmental effects on the total variance of a phenotype

    • ADE or ACE Models

  • 3- Test ADE (ACE) submodels to identify and report significant genetic and environmental contributions

    • AE or E Only Models





Bmi twin correlations1

0.78 data...or do we?

0.30

BMI Twin Correlations

A = 2(rMZ-rDZ)

C = 2rDZ - rMZ

E = 1- rMZ

ADE or ACE?


Giving the ace model a try if there is time
Giving the ACE Model a Try data...or do we?(if there is time)

I think I would like to have the class “help” me put the ADE model together and run. However, I do have code ready for them to work on.


Goodness of fit statistics1
Goodness-of-Fit Statistics data...or do we?


Goodness of fit statistics2
Goodness-of-Fit Statistics data...or do we?


Estimated values5
Estimated Values data...or do we?


Estimated values6
Estimated Values data...or do we?


Conclusions
Conclusions data...or do we?

  • BMI in young OZ females (age 18-30)

    • additive genetic factors: highly significant

    • dominance: borderline significant

    • specific environmental factors: significant

    • shared environmental factors: not


Potential complications
Potential Complications data...or do we?

  • Assortative Mating

  • Gene-Environment Correlation

  • Gene-Environment Interaction

  • Sex Limitation

  • Gene-Age Interaction


For Your Reference: An Overall Map of the How Open Mx Processes Built the ADE Model as Coded in twinADEcon.R

Make matrices

pathA, pathD, pathE

Do Matrix Algebra w Matrices

covA, covD, covE, covMZ,covDZ

Call Data for Use in the ModeldataMZ, dataDZ

Call Data for Use in the ModeldataMZ, dataDZ

Build Model from Matrices/Algebras

modelMZ, modelDZ

Build/Complie Overall Model from Matrices/Algebras

AdeModel

Run Overall Model

AdeModel

Get Summary Information from Overall Model

AdeSumm

Generate Parameter Estimates from Overall Model

estMean, estCovMa, estCovDZ


Thank you
Thank You! Processes Built the ADE Model as Coded in twinADEcon.R


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