Main description:

This volume focuses on the use of system genetic methods and the use of murine models to study the role of gene variants and environmental factors on human health and disease-what is now often called personalized or precision health care. The protocols in this book will help readers analyze genetic causes of heritable variation across a wide range of systems and traits using rodent models. The chapters in this book are separated into three sections that cover: 1) resources for systems genetics; 2) tools for analysis and integration in systems genetics; and 3) systems genetics use cases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

Practical and thorough, Systems Genetics: Methods and Protocols is a valuable resource for anyone who is interested in this diverse field.

Contents:

Part I Resources for Systems Genetics

1. Resources for Systems Genetics
Robert W. Williams and Evan G. Williams

2. Heterogeneous Stock Populations for Analysis of Complex Traits
Leah Solberg Woods and Richard Mott

Part II Tools for Analysis and Integration in Systems Genetics

3. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research
Janan T. Eppig, Cynthia L. Smith, Judith A. Blake, Martin Ringwald, James A. Kadin, Joel E. Richardson, and Carol J. Bult

4. GeneNetwork: A Toolbox for Systems Genetics
Megan K. Mulligan, Khyobeni Mozhui, Pjotr Prins, and Robert W. Williams

5. Complex Trait Analyses of the Collaborative Cross: Tools and Databases
Ramesh Ram and Grant Morahan

6. Integrative Functional Genomics for Systems Genetics in GeneWeaver.org
Jason A. Bubier, Michael A. Langston, Erich J. Baker, and Elissa J. Chesler

7. A Suite of Tools for Biologists that Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel
Christoph D. Rau, Mete Civelek, Calvin Pan, and Aldons J. Lusis

8. Expression QTLs Mapping and Analysis: A Bayesian Perspective
Martha Imprialou, Leonardo Bottolo, and Enrico Petretto

9. Epigenetics and Control of RNAs
Henrike Maatz, Sebastiaan van Heesch, Allison Faber, Franziska Kreuchwig, Eleonora Adami, Norbert Hubner, and Matthias Heinig

10. Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes
Rupert W. Overall

11. RNA-Seq in the Collaborative Cross
Richard Green, Courtney Wilkins, Martin T. Ferris, and Michael Gale, Jr.

12. QTL Mapping and Identification of Candidate Genes in DO Mice: A Use Case Model Derived from a Benzene Toxicity Experiment
Dan Gatti, John E. French, and Klaus Schughart

13. Visualization of Results from System Genetics Studies in Chromosomal Context
Karen Y. Orostica and Ricardo A. Verdugo

Part III Systems Genetics Use Cases: Mapping and Combining Multiple Phenotypic Traits in Mouse Genetic Reference Populations

Organ Systems

14. Genomic Control of Retinal Cell Number: Challenges, Protocols, and Results
Patrick W. Keeley, Irene E. Whitney, and Benjamin E. Reese

15. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene
Sumana R. Chintalapudi and Monica M. Jablonski

16. Genetic Dissection of Variation in Hippocampal Intra-and Infrapyramidal Mossy Fibers in the Mouse
Anna Delprato and Wim E. Crusio

17. Complex Genetics of Cardiovascular Traits in Mice: F2-Mapping of QTLs and their Underlying Genes
Svitlana Podliesna, Connie R. Bezzina, and Elisabeth M. Lodder

18. Systems Genetics of Live Fibrosis
Rabea A. Hall and Frank Lammert

Metabolism

19. Systems Genetic Analysis of Iron and its Regulation in Brain and Periphery
Byron C. Jones and Leslie C. Jellen

20. Systems Genetics of Obesity
Sebastian Heise, Danny Arends, Ayca Dogan, and Gudrun A. Brockmann

Behavior

21. Social Interactions and Indirect Genetic Effects on Complex Juvenile and Adult Traits
David G. Ashbrook and Reinmar Hager

22. Complex Genetics of Behaior: BXDs in the Automated Home-Cage
Maarten Loos, NeuroBsik Mouse Phenomics Consortium, Matthijs Verhage, Sabine Spijker, and August B Smit

23. Integrative Analysis of Genetic, Genomic and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets
James W. Bogenpohl, Kristin M. Mignogna, Maren L. Smith, and Michael F. Miles

Infectious Diseases

24. Dissection of Host Susceptibility to Bacterial Infections and its Toxins
Aysar Nashef, Mahmoud Agbaria, Ariel Shusterman, Nicole Ivan Lore, Alessandra Bragonzi, Ervin Wiess, Yael Houri-Haddad, and Fuad A. Iraqi

25. The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases
Paul L. Maurizio and Martin T. Ferris

From Traits to Networks

26. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, and Enrico Petretto

27. Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits
Laura Saba, Paula Hoffman, and Boris Tabakoff

28. Precise Network Modeling of Systems Genetic Data Using the Bayesian Network Webserver
Jesse D. Ziebarth and Yan Cui

Translation to Human

29. Using Systems Genetics to Understanding the Etiology of Complex Disease
Ramesh Ram and Grant Morahan