Summer School 2026: Bases and Computing Techniques for Genomic Predictions and GWAS
Dates: September 14 - 17, 2026
Time: from 9:00 AM to 5:00 PM
Place: University of Goettingen
Department of Animal Sciences
Albrecht-Thaer-Weg 3
37075 Göttingen
Local Organising Committee:
Dr. Lisa Maria Rienesl (lisa.rienesl@uni-goettingen.de)
Prof. Dr. Christine Große-Brinkhaus, Head of the department
Brief description: This course encompasses the background needed to perform genomic
analyses used in Animal Breeding and Genetics with the BLUPF90 programs (Misztal et al.,
2014).
Day 1:
- Introduction of BLUPF90 family of programs for the analyses of mixed models including single and multiple traits, maternal effects, and repeatability models
- Renumbering datasets: renumf90
- Estimation of breeding values and VCE: blupf90+
- Estimation of breeding values and VCE - Bayesian: gibbsf90+
- Exercises: use of BLUPF90 programs with real data for single and multiple trait models
Day 2:
- Introduction to Genomic data
- History of the use of genomic data
- Genomic markers
- Statistics of genomic data
- Genomic files
- Quality control for SNP data, genomic and pedigree relationships
- Call rate
- Parental exclusions
- Distributions of diagonals and off-diagonals of G
- Differences between matched G and A22
- Eigenvalues/eigenvectors – population stratification
- preGSf90 and qcf90 for quality control
- Bash scripting to deal with genotypes, pedigree, and phenotypes
- Exercise: Data editing with bash scripting and quality control of genomic data
Day 3:
- Introduction to Genomic Selection
- Theory of Single-step GBLUP (ssGBLUP)
- Creating and handling genomic relationship matrices with preGSf90
- Validation techniques for testing genomic models
- Prediction accuracy vs. theoretical accuracy
- Prediction accuracy with and without validationf90
- Exercises: Use of ssGBLUP with BLUPF90 programs in simulated datasets andvalidation of genomic predictions
Day 4:
- Estimating SNP effects from GBLUP and ssGBLUP models
- Indirect predictions using SNP effects
- Weighted GBLUP and ssGBLUP
- Single-step Genome-wide association studies (GWAS)
- Exercises: Compute SNP effects from ssGBLUP, run indirect predictions for young animals, and do ssGWAS (variance explained by SNP and p-values) with BLUPF90 programs
Requirements / Prerequisites
- Participants must bring their own laptop with the BLUPF90 software family pre-installed
- Installation instructions and download available here: https://nce.ads.uga.edu/wiki/doku.php?id=start
- Basic knowledge of animal breeding, quantitative genetics and genomics (e.g. genetic evaluation, SNP data)
- Basic computational skills, including familiarity with command-line environments and handling of data files
Participation fees:
Master students from University of Goettingen € 50
PhD students from University of Goettingen € 70
All other Master students € 60
All other PhD students € 90
Postdocs € 100
*including course material , coffee, drinks and snacks during course times (additional meals and accommodation are not included)
Please click here to register for your seat!
Optional Mandatory pre-course:
Basics of mixed model equation, genomic prediction, and genome-wide association studies (GWAS)
Date: August 31 - September 1, 2026
Time: From 9:00 AM to 4:00 PM
Place: Georg-August University Göttingen, Department of Animal Sciences
Instructor: Prof. Dr. Christine Große-Brinkhaus
Purpose:
This optional pre-course aims to prepare participants for the summer school “Fundamentals and computational methods for genomic prediction and genome-wide association studies (GWAS)” by refreshing the basic concepts of mixed model equation, genomic prediction, and GWAS, and by providing background information. Further, a brief check on technical requirements to work with the BLUPF90 programs will be offered.