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On Biostatistical Genetics Using Twin Data Jacob Hjelmborg University of Southern Denmark Fall 2013 Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 1 / 63

Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

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Page 1: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

On Biostatistical GeneticsUsing Twin Data

Jacob Hjelmborg

University of Southern Denmark

Fall 2013

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 1 / 63

Page 2: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 2 / 63

Page 3: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

The Danish Twin RegistryThe oldest twin registry

Founded in 1953 by doctors Tage Kemp, Mogens Hauge and BentHarvald.Cancer among initial focuses. Rockefeller Foundation and NIH∼100.000 twins born from 1870 till now.Population based with more than 97% completeness.Linked to National Registries.

Page 4: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

The Danish Twin Registry

Page 5: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

The Danish Twin Registry

Page 6: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Twin Symposium 2013

Page 7: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

BRCA gene discoverer

Mary-Claire KingPioneer in research into hereditary breast cancer: New Scientist June2013

’Supreme court is right - the BRCA1 gene cannot be patented’.Portrayed in forthcoming film ’Decoding Annie Parker’.’Tales of a Minstrel Geneticist’ - Title of this year’s Hans ChristianAndersen lecture at the University of Southern Denmark, ThursdayNovember 14th.

Page 8: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

1

2

3

1

2

3

1

2

3

1

2

3

1

2

3

1

2

3

Males

Females

3.0

53.1

3.1

53.2

3.2

5M

ean lnB

MI

15 20 25 30 35 40 45 50 55 60 65Mean age

Longitudinal BMI

Body Mass IndexUS Twin Study 1997: Genetic influences on changes in body mass index:a longitudinal analysis of women twins. (Mary-Claire King)Finnish Twin Study 2007: Genetic influences on growth traits of BMI: alongitudinal study of adult twins.modeling change: BMI(t)i = αi + βi tSee K. Holst ’Day1-estimation’ slide: Longitudinal Biometric Analysis

Page 9: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 9 / 63

Page 10: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

What is heritability?

Darwin: Origin of the Species (1859)The inherited traits form the basis for natural Selection, Mutation andReplication.

The inherited is a blend

Page 11: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Mendel: Experiments in Plant Hybridization (1865)The inherited is a fifty-fifty mix of discrete units.

Mendel’s First Law (Segregation): One allele of each parent is randomlyand independently selected, with probability 1

2 , for transmission to theoffspring. The alleles unite randomly to form the offspring’s genotype.Mendel’s Second Law (Independent Assortment): The alleles underlyingtwo or more different traits are transmitted to offspring independently ofeach other. The transmission of each trait separately follows the first lawof segregation.

How can Mendel’s discrete units explain the variation in continuous humancharacteristics?

Page 12: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Statistical geneticsHow is variation at phenotypic level governed by variation at genetic level?

Two structures for modelling: mean and variance-covariance.R.A. Fisher (1918): The variance-covariance matrix varies by type of twinpairs.

Σ =

(variance of first twin covariance of twinscovariance of twins variance of second twin

)-a measure of twin similarity: ρ, correlation (K. Pearson 1904)

Page 13: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Aims

Difference in correlations between MZ and DZ twins suggests geneticinfluence on trait.What type and magnitude of genetic and environmental influences toexpect?Classical twin analysis using the polygenic model, known as theADCE-model, in which the individual outcome, Yi decomposes into

Yi = Ai + Di + Ii + Ci + Ei ,

whereI A: Additive genetic effects of allelesI D: Dominant genetic effectsI I: Epistasis genetic effectsI C: Shared environmental effectsI E : Unique environmental effects

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 13 / 63

Page 14: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Biometric analyses - polygenic model (Falconer 1981)

Contributing factors to the variation in outcome:

ΣY =

(σ2

A zσ2A

zσ2A σ2

A

)+

(σ2

D uσ2D

uσ2D σ2

D

)+

(σ2

I kσ2I

kσ2I σ2

I

)+

(σ2

C σ2C

σ2C σ2

C

)+

(σ2

E 00 σ2

E

)where z = u = k = 1 for MZ pairs, z = 1

2 , u = 14 and 0 ≤ k ≤ 1

4 for DZ pairs.

In particular, we obtainHeritability:

H2Y =

σ2A + σ2

D + σ2I

σ2A + σ2

D + σ2I + σ2

C + σ2E

= h2 + d2 + i2

Shared environmental effect:

C2Y =

σ2C

σ2A + σ2

D + σ2I + σ2

C + σ2E

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 14 / 63

Page 15: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

H2 Heuristics {ρMZ = h2 + d2 + i2 + c2

ρDZ = 12 h2 + 1

4 d2 + ki2 + c2

HenceρMZ − ρDZ ≤ H2 ≤ min{ρMZ ,2(ρMZ − ρDZ )}

If no epistasis, {ρMZ = h2 + d2 + c2

ρDZ = 12 h2 + 1

4 d2 + c2

we obtain43

(ρMZ − ρDZ ) ≤ H2 ≤ min{ρMZ ,2(ρMZ − ρDZ )}

Heritability propositionsH2 = 0 always if ρMZ = ρDZ , hence existence of genetic effects can bedetected solely from correlations and is robust towards misspecificationof genetic model, nice!H2 differs by at most ρMZ − ρDZ from true value.

Page 16: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Correlation heuristics

Within pair similarity is measured by correlations.Correlations are further modelled by genetic and environmental variancecomponents via the polygenic ADCE model.For instance, the polygenic ACE model relates to correlations viaρmz = h2 + c2 and ρdz = 1

2 h2 + c2.

Heuristics of MZ and DZ correlationsInterpretation

Relation Genetics Environment Examplesρmz > 4ρdz Epistasis albinismρmz > 2ρdz Genetic dominance Dρmz = 2ρdz Additive effect A (mono- or polygenic) and small D Small C BMI2ρdz > ρmz > ρdz Additive genes A Shared environment C longevityρmz = ρdz > 0 No genetic effect Cρmz = ρdz = 0 No genetic effect No familial aggregation

Page 17: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Biometric analyses - polygenic modelMain assumptions

Equal environments assumption for MZ and DZ twins.No gene-environment interaction and correlation.No gene-gene interaction (link: epistasis).Equal mean and variance of twin 1 and twin 2, MZ and DZ.Estimation and inference by maximum likelihood principle assumingbivariate normality of paired observations (as before).

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2.8 3.0 3.2 3.4 3.6

2.8

3.0

3.2

3.4

3.6

ext$logbmi.1[ext$zyg == "MZ"]

ext$

logb

mi.2

[ext

$zyg

==

"MZ"

]

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2.8 3.0 3.2 3.4 3.6

2.8

3.0

3.2

3.4

3.6

ext$logbmi.1[ext$zyg == "DZ"]

ext$

logb

mi.2

[ext

$zyg

==

"DZ"

]

Page 18: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 18 / 63

Page 19: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Sex-limitation model to include OS DZ’s

Should we include opposite sexed DZ’s?Are the same genes in males and females affecting the trait of interest?(genetic pleiotropy)-howto?

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 19 / 63

Page 20: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Example

Height difference between men and womenMen are taller than women.Is this because of genetic differences?

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 20 / 63

Page 21: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Height difference between men and women

Within pair correlations for same and opposite sex DZ twins

Within pair correlationcountry DZ males DZ females OS twinsAustralia 0.42 0.49 0.46Denmark 0.47 0.55 0.50Finland (old) 0.50 0.49 0.49Finland (young) 0.53 0.53 0.49Italy 0.57 0.49 0.30The Netherlands 0.47 0.49 0.43Norway 0.49 0.49 0.44

source: Silventoinen et al., Twin Res 2000 and 2003

There is no significant difference between correlations within SSDZ andOSDZ twin pairsThere seems to be no sex-specific genetic factor affecting height.

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 21 / 63

Page 22: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Sex-limitation model to include OS DZ’s

Studying gene×gender interaction.Making use of all DZ pairs.

The within-pair covariance of male and female twins:

Cov(male,female) = gσAmσAf + σCmσCf

Will g = 12 as for DZ same sex pairs?

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 22 / 63

Page 23: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Sex-limitation model to include OS DZ’s

DZSS Males,

ΣDZSS =

(σ2

Am+ σ2

Cm+ σ2

Em

12σ

2Am

+ σ2Cm

12σ

2Am

+ σ2Cm

σ2Am

+ σ2Cm

+ σ2Em

)DZSS Females,

ΣDZSS =

(σ2

Af+ σ2

Cf+ σ2

Ef

12σ

2Af

+ σ2Cf

12σ

2Af

+ σ2Cf

σ2Af

+ σ2Cf

+ σ2Ef

)DZOS,

ΣDZOS =

(σ2

Am+ σ2

Cm+ σ2

EmgσAmσAf + σCmσCf

gσAmσAf + σCmσCf σ2Af

+ σ2Cf

+ σ2Ef

)

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 23 / 63

Page 24: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Sex-limitation model to include OS DZ’s

We will encounter more examples as we go along.A value of g = 1

2 for OS twins suggest no gender specific genetic effect.-a lower value will indicate such effects.R package ’mets’ estimates g when OS pairs are available.See K. Holst ’Day1-estimation’ slide: Gene-Environment Interactions.

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 24 / 63

Page 25: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 25 / 63

Page 26: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Review of classic twin analysis aims and methodology

Inferring genetic influence without observing any gene.What is the contribution of genetic and environmental factors to thevariation?Are the same or different genes influencing the traits?{

Y = Genes + EnvironmentΣY = ΣGenes + ΣEnvironment

However, there are other fruitful use of collections of twin pairs.

SEE SLIDES: "Day02caseCotwin.pdf“.

Page 27: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 27 / 63

Page 28: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

What is dependence?

AimTwin studies may provide a frame for genetic analysis and etiology.For instance in the etiology of cancer.A measure of dependence becomes utterly important.

CorrelationF. Galton (1890)

’I can only say that there is a vast field of topics that fall underthe laws of correlation, which lies quite open to the research ofany competent person who cares to investigate it’

Page 29: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Pearson 1904The product moment correlation

E{(X − µ)(Y − µ)}Measures linear dependence.

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6080

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time.2

time.

1

R.A. Fischer 1918Heritability in terms of correlations.Genetic variation causing phenotypic variation

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Variance explained by SNPs in metabonomic traits

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Addendum

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 31 / 63

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Agouti MZ mice

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Equal but not the same

The Epigenetics RevolutionControlled reading of DNADetermines function of cellMay change during lifeTransgenerational inheritance(!) (Lamarckism?).Ovrekalix, Dutch famine, Obesity mice, . . .

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Equal but not the same

Epigeneticsmakes monozygotic twins different from first replicationkey in evolutionary dynamics of cancer

Schewig et. al. , Max Planck Berlin, 2013

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Equal but not the same

In parallel: Evolutionary dynamicsEvolutionary dynamics: Replication, Mutation and Selection.Statistical genetics governs mostly Mutation and Selection.Epigenetics: Replication of genetic Information.

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Epigenetic treatment of acute leukemia by5-aza-cytidine

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Equal but not the same

Epigenetics in Twin Studies1 Genetics of Epigenetics (genetic influences on epigenetic effects)2 Epigenetic Epidemiology (case-cotwin discordance)

AimHeritability of complex traits?-for instance taking epigenetic phenomena into account.In general: non-Mendelian inheritance?, genetic variation with time?

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’MZ Nokia mobile phones’

What is the conveyed information between X and Y?

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Information Theory

The Mutual Information

I(X ,Y ) =

∫∫fXY (x , y) log

fXY (x , y)fX (x)fY (y)

dxdy

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E. H. Linfoot 1957

Theorem: E.H. Linfoot (1957)For (X ,Y ) ∼ F ,

ν(X ,Y ) =√

(1− exp(−2I(X ,Y )))

where I(X ,Y ) =∫∫

fXY (x , y) log fXY (x,y)fX (x)fY (y)

dxdy is the mutual information,satisfies the seven correlation properties of Renyi.

Renyi propertiesIndependence if and only if ν(X ,Y ) = 0Strict dependence if and only if ν(X ,Y ) = 1Bivariate Gaussian: Linfoot is |ρ(X ,Y )|Invariance under continuous and strictly increasing marginaltransformations

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Information

The Informational CorrelationThe Linfoot transform of the Mutual Information is bridging Informationtheory with Statistics.

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Generalizing heritability (joint with A. Kryger Jensen)We propose:

The informational heritability coefficient

h2∗ = 2(LMZ(X ,Y | XMZ)− LDZ(X ,Y | XDZ))

L(X ,Y ) =√

1− exp(−2I(X ,Y )) (Linfoot’s correlation)

I(X ,Y ) =

∫∫log

f (x , y)

f (x)f (y)dF (x , y) (Mutual Information)

PropertiesMarginal densities may be constrained to be exchangeable within pairsand equal for MZ and DZ types of pairsProposition: h2

∗ generalizes classic Falconer h2 for bivariate normalsh2∗ is measuring proportion of density explained by genetic variations

transmitted to phenotypic density patterns.topology may be rather complex.

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Perspectives

Epigenetics: Key in evolutionary dynamics of cancer. Evidence fortransgenerational inheritance.Calls for more general heritability measure.Linfoot’s correlation is based on the mutual information and fulfills Renyiproperties.

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Overview

1 Introduction

2 Heritability Heuristics and History

3 Opposite versus Same Sexed Pairs

4 The Matched Case-Cotwin Design and Analysis

5 On Epigenetics and Information Theory in Twin Studies

6 Examples

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 44 / 63

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Example 1: Bivariate Gaussian simulation

Twinlm Falcon h*

0.0

0.2

0.4

0.6

0.8

1.0

500 simulations with 300 MZ and 300 DZ pairs

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Agouti MZ mice

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simulation

-3 -2 -1 0 1 2 3

-3-2

-10

12

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Twinlm Falcon Kendall Spearman h*

0.0

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500 simulations with 300 MZ and 300 DZ pairs

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Albumin - h2 = 0 (Bathum et al. 2004)

0.2 0.4 0.6 0.8

0.2

0.4

0.6

0.8

MZ Albumine levels

Twin

Co−

Twin

0.5

0.5

1

1.5

1.5

1.5

2

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Albumin - h2 = 0 (Bathum et al. 2004)

0.0 0.2 0.4 0.6 0.8 1.0

0.2

0.4

0.6

0.8

1.0

DZ Albumine levels

Twin

Co−

Twin

0.5

0.5 1

1.5

1.5

2

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Albumin - h2 = 0 (Bathum et al. 2004)

Proposed heritability for general associationsLMZ = 0.47LDZ = 0.30

h2∗ = 0.34

-estimation needs to be validated!

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Time to event twin dataMain objectives:

I Time-varying genetic influenceI Taking censoring and competing risks into account,

Major component in NorTwinCan Study joint with

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The Nordic Twin Cancer Study

∼ 400.000 Nordic twins linked with national cancer registries.42 common cancer sites:

1 "Lip"2 "Tongue"3 "Salivary glands"4 "Mouth"5 "Pharynx"6 "Oesophagus"7"Stomach"8 "Small intestine"9 "Colon"10 "Rectum and anus"11 "Liver"12"Gallbladder and extrahepatic bile ducts"13 "Pancreas"14 "Nose, sinuses"15"Larynx"16 "Lung (incl. trachea and bronchus)"17 "Pleura"18 "Breast"19"Cervix uteri"20 "Corpus uteri"21 "Uterus, other"22 "Ovary and uterineadnexa"23 "Other female genital organs"24 "Prostate"25 "Testis"26 "Penisand other male genital organs"27 "Kidney"28 "Bladder and other andunspecified urinary organs"29 "Melanoma of skin"30 "Skin, non-melanoma"31"Eye"32 "Brain, central nervous system"33 "Thyroid"34 "Bone"35 "Softtissues"36 "Non-Hodgkin lymphoma"37 "Hodgkin’s disease"38 "Multiplemyeloma"39 "Acute leukaemia"40 "Other leukaemia"41 "All sites butnon-melanoma skin"42 "All sites - first diagnosis"60 "Rectum"61 "Colorectal"

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Multiple outcome at time t .

alive

dead

prostate cancer

α01(t)

α02(t)

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 53 / 63

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Cumulative incidence

40 50 60 70 80 90 100

0.00

0.05

0.10

0.15

Age

Cum

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Inci

denc

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DenmarkFinlandNorwaySweden

The cumulative incidence function:

Fcancer(t) = Prob(T ≤ t , ε = cancer) =∫ t

0λcancer(s)S(s−)ds,

NB! Same prostate cancer mortality (Bray et al. Eur Jour Cancer 2010).

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Concordance

Scheike et al. 2013: Semi-parametric random effects regression model ofthe cumulative incidence function.The concordance function conditional on covariates

P(T1 ≤ t , ε1 = cancer,T2 ≤ t , ε2 = cancer|X ),

Dependence in terms of: Probandwise concordance, relative recurrencerisk, cross-odds ratio and multilocus index.Alternative frailty approach on hazard scale by F. Eriksson (2013).

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 55 / 63

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Prostate cancer - Nordic - Concordance

60 70 80 90 100

0.0

0.1

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0.3

0.4

0.5

Age

conc

orda

nce

60 70 80 90 100

0.0

0.1

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0.5

Age

conc

orda

nce

Probandwise concordance

MZ pairsDZ pairsIndependence

Methods: Estimating heritability for cause specific mortality based on twin studies. Scheike,Holst and Hjelmborg, LIDA (2013).

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Bivariate extreme value theory

-joint with J. Kaprio, Y. Goegebeur and M. Osmann.M. Osmann receives "Dansk Matematisk Forenings specialepris for 2012"

Biostatistics (Institute of Public Health) On Biostatistical Genetics Fall 2013 57 / 63

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Extreme value theory for twin dataObesity

Evidence for epigenetic effects governing extreme BMI (Obesity).Twin studies can provide a frame for genetic analysis and etiology.Modelling the dependence of extremes becomes utterly important.

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20 30 40 50 60

1520

2530

3540

Age

BM

I

Page 59: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Upper tail copulas

Twin

Co−

Twin

BM

I density

Twin

Co−

Twin

BM

I density

Page 60: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Dependence measures for upper tail

N η χ χ L(X ,Y ) h2∗

MZ Overall 20048 0.80 0.49 0.59 0.23 0.24Men 8212 0.78 0.45 0.56 0.22 0.13

Men (Age 18-29) 2241 0.83 0.44 0.67 0.29 0.57Men (Age 30-39) 3356 0.87 0.41 0.74 0.13 0.21Men (Age 40-60) 2615 0.70 0.39 0.39 0.22 0.14

DZ Overall 37476 0.61 0.26 0.21 0.11 -Men 16354 0.60 0.22 0.20 0.16 -

Men (Age 18-29) 4356 0.60 0.22 0.20 0.00 -Men (Age 30-39) 6657 0.55 0.16 0.10 0.03 -Men (Age 40-60) 5341 0.65 0.14 0.30 0.15 -

Page 61: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Practical: Estimating upper tail dependence measures

This session illustrates how to estimate the upper tail dependence measure

χ = limu→1

Prob(U1 ≥ u | U2 ≥ u)

from the classical bivariate extreme value distribution.

Bivariate Extreme Value DistributionLauch R-code on next slide to obtain an estimate of χEstimate χ for MZ and for DZ pairs.

Reference: Coles S, "An Introduction to Statistical Modeling of Extreme Values", Springer (2001).

Page 62: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

Fitting Bivariate Peaks Over a Threshold Using Bivariate Extreme ValueDistributions

library(POT)library(mets)

data(twinbmi)

# a number, 1 or 2, is assigned to each twin in a pair.twinbmi$nr <- with(twinbmi, ave(bmi,tvparnr, FUN = seq_along))twinbmi$logbmi <- log(twinbmi$bmi)

bmiwide <- reshape(twinbmi,idvar="tvparnr",timevar="nr",v.names=c("bmi","logbmi","age"),direction="wide")

th = quantile(twinbmi$bmi,probs=0.80, na.rm=TRUE)

extlog <- fitbvgpd(cbind(bmiwide$bmi.1,bmiwide$bmi.2),c(th,th),cshape=TRUE, cscale=TRUE,model = "log")

extlog$chi

Page 63: Using Twin Data Jacob Hjelmborg - staff.pubhealth.ku.dkstaff.pubhealth.ku.dk/~kkho/undervisning/family2013/biostatgen.pdf · On Biostatistical Genetics Using Twin Data Jacob Hjelmborg

The R kiosk

’mets’ (K. Holst, T. Scheike)’etm’ (A. Allignol); ’prodlim’ (T. Gerds).