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Whole-genome evaluation of complex traits using SNP, haplotype, or QTL information

Gorjanc G. & Hickey J. M.

Genetika 2012, Maribor, Slovenia

Introduction
Whole-genome technologies rich data

In complex traits (e.g., body height, weight, ) gene discovery still very limited Rich genome-wide data can be used for prediction
(classicaly based on phenotype and pedigree data)

AIM: Show the value of different types of information for prediction in complex traits

Different sources of information


(simplistic scheme)
k-1 k k+1 k+2 k+3 k+4 k+5 k+6

+0 cm

C G C G C G C G C G C G

C G C G C G T A T A T A

T A T A T A C G C G C G

A T A T A T A T A T A T

G C G C G C G C T A T A

A T A T A T A T A T A T

Haplotypes

+1 cm

+2 cm

SNP QTL

SNP

Methods - Idea

Methods - Simulation

Methods Simulated data


Gen. 1 2 Calibration Validation

3
4 5 6 7 8 9 Genotype Pedigree Genotype Genotype Phenotype

AGV

10

Genotype

Methods Statistical analysis

GWAS vs. relationship modelling


GWAS

Relationships use the same underlying information (phenotype and genotype data) to infer the sum of all GWAS estimates

Haplotype similarity
Long haplotypes explosion in #haplotypes
k-1 k k+1 k+2 k+3 k+4 k+5 k+6

C G C G C G

C G T A T A

T A C G C G

A T A T A T

G C G C T A

A T A T A T

But parts of haplotypes are similar efective number of haplotypes is smaller Similarities Haplotype 1 Haplotype 2
(several variations tested)
Haplotype 1 Haplotype 2 Haplotype 3 6/6 4/6 6/6

Haplotype 3 3/6 5/6 6/6

Results Gaussian QTL


Haplotypes no similarity

QTL

QTL

Pedigree SNP V

SNP Y Haplotypes similarity 2

Haplotypes similarity 1

Results Gamma QTL


Haplotypes no similarity

QTL

QTL

Pedigree SNP V

SNP Y Haplotypes similarity 2

Haplotypes similarity 1

Conclusions
Genome-wide information increases accuracy in comparison to classic methods using pedigrees and phenotypes only Long haplotypes large #haplotypes
low accuracies similarities help no advantage over SNP data (perhaps due to large #haplotypes)

Accuracies drop in further generations (not so much with Gamma QTL data) can not predict distant relatives or unrelated individuals accurately!!!
Even with QTL data accuracies are not perfect!!!

Whole-genome evaluation of complex traits using SNP, haplotype, or QTL information


Gorjanc G. & Hickey J. M.

Genetika 2012, Maribor, Slovenia