Systems Genetics for Experimental Crosses

• Tentative Schedule for 2012
• 2012 Notes in Preparation
• 2012 Tutorial Material
• Pertinent Notes from Other Talks
• Previous Talks and Relevant Material
• Workflow Platforms for Systems Genetics
• References

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

• Module 15 Lecture Handout (separated by session below as PDF)

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

• Module 15 Tutorial Handout

• R/qtl & R/qtlbim Tutorials
  • qtl R code & Broman's qtl tutorials
  • R/qtl Package at CRAN
  • qtlbim R code & qtlbim vignette
  • R/qtlbim Package at CRAN
• R/qtlhot Tutorial
  • qtlhot R code & qtlhot vignette
  • R/qtlhot Package at CRAN
• R/qtlcmst Tutorial
  • qtlcmst R code & qtlcmst vignette
  • qtlcmst raw R functions
  • R/qtlcmst package at GITHUB (Windows-ready package)
• R/qtlnet Tutorial
  • qtlnet R code & qtlnet vignette
  • R/qtlnet Package at CRAN

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

• SISG Advanced QTL Mapping, 2011
• Jackson Labs Causal Network Models for Correlated Quantitative Traits, 2011
• Jackson Labs Bayesian Model Selection for Multiple QTL, 2009
• MSRC5: Quantile Based Permutation Thresholds for QTL Hotspots, 2012
• U NC Systems Genetics, 2010
• Sage Systems Genetics, 2010
• Yandell talks

References

• Chaibub Neto E, Ferrara C, Attie AD, Yandell BS (2008) Inferring causal phenotype networks from segregating populations. Genetics 179: 1089-1100.
• Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann Appl Statist 4: 320-339.
• Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2012) Causal model selection hypothesis tests in systems genetics. Genetics (in review). [earlier version as 2010 TR 1157]
• Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for QTL hotspots. Genetics 191: 000-000 (accepted).
• Ferrara CT, Wang P, Chaibub Neto E, Stevens RD, Bain JR, Wenner BR, Ilkayeva OR, Keller MP, Blasiole DA, Kendziorski C, Yandell BS, Newgard CB, Attie AD (2008) Genetic networks of liver metabolism revealed by integration of metabolic and transcriptomic profiling. PLoS Genet 4: e1000034.
• Moon JY, Chaibub Neto E, Deng X, Yandell BS (2011) Growing graphical models to infer causal phenotype networks. In Probabilistic Graphical Models Dedicated to Applications in Genetics. Sinoquet C, Mourad R, eds. (in review)