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 (dougspeed.com)

2 Centre for Systems Genomics (sysgenmelb.org)

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

 

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

 

Schedule

 

Slides

 

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)

 

 

Data

Module 4 data

Module 6 data

Module 7 data

 

 

DSC01227

 

DOWNLOAD GROUP PHOTO

 

 

IMG_3931

 

IMG_3929

 

 

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.

 

MATERIALS PREVIOUS SUMMER COURSES

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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