Armidale Genetics Summer Course 2016

University of New England, Armidale, NSW Australia



Investigating the Genetic Architecture of Complex Traits

& Prediction of Phenotype from Genome-wide SNPs


Teachers: Doug Speed1 and David Balding2

1 University College London (

2 Centre for Systems Genomics (

and Schools of BioSciences and Maths & Stats, University of Melbourne


Dates: Monday 1 February 2016 (9am) - Friday 5 February 2016 (4pm)






2. Introduction to PLINK and QC

3. Basic Association Analysis

4. PLINK and QC Practical

5. Advanced association

6. Practical Association Studies

7. Traditional Heritability

8. Relatedness

9. SNP based heritability analysis

10. Practical SNP heritability

11. Genomic Prediction

13. Bessie (Vinzent)

14. Extension to estimating h2

15. Prediction Practical


17. MTG2 Presentation (Hong)

17b. MTG2 Practical

18. Practical extensions

20. Genomic prediction for selection (Julius)




Module 4 data

Module 6 data

Module 7 data













Participants should be familiar with R, at least through an online tutorial. They should bring a good-spec laptop with R pre-installed. Ideally they should also be familiar with PLINK and IMPUTE2, but refreshers and other help will be given for R, PLINK and IMPUTE2. GCTA and LDAK will be introduced with no prior knowledge assumed.



Armidale Animal Breeding Summer Course 2015 Materials

         Primer to genomic analysis using R: Cedric Gondro

         From Sequence Data to Genomic Prediction: Ben Hayes and Hans Daetwyler

Armidale Animal Breeding Summer Course 2014    Materials

        Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf

Armidale Animal Breeding Summer Course 2012    Materials

         Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos

Armidale Animal Breeding Summer Course 2011    Materials

         Statistical methods and design in plant breeding and genomics: Ian Mackay

        IBD inference in genome association studies: Elizabeth Thompson

Armidale Animal Breeding Summer Course 2010    Materials

         Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics: Brian Kinghorn, Cedric Gondro

         Bayesian methods in genome association studies: Dorian Garrick,  Rohan Fernando

Armidale Animal Breeding Summer Course 2009    Materials

        Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

         Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma

Armidale Animal Breeding Summer Course 2008      Materials 

         Genomic Selection:       Ben Hayes

Armidale Animal Breeding Summer Course 2007      Materials

         Generalized Linear Mixed Models:       Steve Kachman

Armidale Animal Breeding Summer Course 2006    Materials

         Gene Expression:         Toni Reverter

         Breeding Program Design:        Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005    Materials
         Breeding Objectives: Gibson, Van der Werf, Kinghorn
         Scientific Writing:          David Lindsay
         ASReml:           Arthur Gilmour
Armidale Animal Breeding Summer Course 2004    Materials
         Bayesian for Beginners               Kerrie Mengersen
         Bayesian Models for QTL analysis        Michel Perez-Enciso
         Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

         Scientific Writing:  David Lindsay
         Linear Models for animal breeding:   Julius van der Werf, Mike Goddard
         QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf
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