Systems Genetics for Experimental Crosses

This is a new course being developed by Brian S. Yandell and Elias Chaibub Neto. It will be given at U WA Seattle's SISG on 23-25 July 2012.

Return to Statistics Genomics Page.

Tentative Schedule for 2012

Monday     23 July 2012
8:30-10    Introductions; Overview of System Genetics
10:30-12   QTL Model Selection
1:30-3     Gene Mapping for Multiple Correlated Traits
3:30-5     Hands On Lab: R/qtl, R/qtlbim
5-6        Reception

Tuesday    24 July 2012
8:30-10    Permutation Tests for Correlated Traits
10:30-12   Scanning the Genome for Causal Architecture
1:30-3     Causal Phenotype Models Driven by QTL
3:30-5     Hands On Lab: R/qtlhot, R/qtlcmst, R/qtlnet
5-6        Tutorial (optional)

Wednesday  25 July 2012
8:30-10    Incorporating Biological Knowledge
10:30-12   Platforms for eQTL Analysis

2012 Notes in Preparation

  1. Overview (PDF)
  2. Model Selection (PDF)
  3. Multiple Traits (PDF)
  4. R/qtl & R/qtlbim Tutorials (see below)
  5. Permutation Tests for Hotspots (PDF)
  6. Causal Model Selection Hypothesis Tests (PDF)
  7. Causal Models (PDF)
  8. R/qtlhot, R/qtlmst & R/qtlnet Tutorials (see below)
  9. Incorporating Biological Knowledge (PDF)
  10. eQTL Platforms (PDF)

2012 Tutorial Material

Pertinent Notes from Other Talks

  1. Model Selection for Genetic Architecture (SISG 2011 pp. 75-136)
  2. Gene Mapping of Multiple Correlated Traits (SISG 2011 pp. 145-164)
  3. Permutation Tests for Omic QTL Hotspots (MSRC 2012)
  4. Platforms for eQTL analysis (SISG 2011 pp. 165-190)
  5. Scanning the Genome for Causal Architecture (new: CMST paper) (ECN in prep)
  6. Causal Phenotype Models Driven by QTL (SISG 2011 pp. 191-204)
  7. Bayesian causal phenotype network incorporating genetic variation and biological knowledge (PPTX) (Oslo 2012)
  8. Computational Infrastructure for Systems Genetics Analysis (UNC 2010)

Previous Talks and Relevant Material


For a more complete set of references on QTL and related subjects, see Yandell's Research & Publications Page or the Statistical Genomics References.
Brian Yandell