2. Complex trait analysis, develop- ment, and genomics The Complex Trait Consortium and the Collaborative Cross Rob Williams, Gary Churchill, and members of the Complex Trait Consortium The Complex Trait Consortium and the Collaborative Cross Rob Williams, Gary Churchill, and members of the Complex Trait Consortium

3. Solving the puzzle of complex diseases, from obesity to cancer, will require a holistic understanding of the interplay between factors such as genetics, diet, infectious agents, environment, behavior, and social structures. Elias Zerhouni: The NIH Roadmap. Science 302:63 (2003) Material included in handouts and on the CD also see www.complextrait.org

4. A group of ~150 mouse geneticists most of whom have interests in pervasive diseases and differences in disease susceptibility. General Aim: Improve resources for complex trait analysis using mice. Main catalysts and models ENU mutagenesis programs Sequencing and SNP consortia What is the CTC Catalyze genotyping of strains Catalyze genotyping of strains Simulation studies of crosses Simulation studies of crosses Planning a collaborative cross Planning a collaborative cross Improved use of resources Improved use of resources

5. 1. Established Nov 2001, Edinburgh (n = 20) 2. 1st CTC Conference, May 2002, Memphis (n = 80; hosted by R Williams) 3. CTC Collaborative Cross design workshop, Aug 2002, JHU (K Broman and R Reeves, host) 4. CTC Satellite meeting at IMGC Nov 2003 (n = 40) 5. 2nd CTC Conference, July 2003, Oxford (n = 80; hosted by R Mott and J Flint) 6. CTC strain selection workshop, Sept 2003 (M Daly, host) 7. 3rd CTC Conference, July 2004, TJL 1. Established Nov 2001, Edinburgh (n = 20) 2. 1st CTC Conference, May 2002, Memphis (n = 80; hosted by R Williams) 3. CTC Collaborative Cross design workshop, Aug 2002, JHU (K Broman and R Reeves, host) 4. CTC Satellite meeting at IMGC Nov 2003 (n = 40) 5. 2nd CTC Conference, July 2003, Oxford (n = 80; hosted by R Mott and J Flint) 6. CTC strain selection workshop, Sept 2003 (M Daly, host) 7. 3rd CTC Conference, July 2004, TJL The short chronology of the CTC

6. Lusis et al. 2002: Genetic Basis of Common Human Disease Are mouse models appropriate? Yes and No. Are mouse models appropriate? Yes and No. If you want to understand where the war on cancer has gone wrong, the mouse is a pretty good place to start. –Clifton Leaf Fortune, March 2004 If you want to understand where the war on cancer has gone wrong, the mouse is a pretty good place to start. –Clifton Leaf Fortune, March 2004

7. Mixing mouse genomes (reluctantly) Current practice: Keep it simple: high power with low n

8. Genetic dissection Aim 1: Convert genetic variation into a small set of responsible gene loci called QTLs. Aim 2: Develop mechanistic insights into virtually any genetically modulated process or disease. Aim 1: Convert genetic variation into a small set of responsible gene loci called QTLs. Aim 2: Develop mechanistic insights into virtually any genetically modulated process or disease. V p = V g + V e + 2(Cov GE) + G X E + V tech V p = V g + V e + 2(Cov GE) + G X E + V tech

9. Standard recombinant inbred strains (RI) C57BL/6J (B) DBA/2J (D) F1 20 generations brother-sister matings BXD1 BXD2 BXD80 + … + F2 BXD RI Strain set BXD RI Strain set fully inbred fully inbred isogenic hetero- geneous hetero- geneous Recombined chromosomes are needed for mapping female male chromosome pair Inbred Isogenic siblings Inbred Isogenic siblings BXDBXD BXDBXD Standard RI strains

10. www.complextrait.org Proposal for a Collaborative Cross

11. 1K Reference Population environment proteomics anatomy pathology anatomy pathology development epigenetic modifications cancer susceptibility transcriptome Meta- analysis metabolism endocrine profile immune response pathogens response pathogens pharmacokinetics physiology Integrative and cumulative analysis/synthesis

12. Broad utility: a resource that combines diverse haplotypes and that harbors a broad spectrum of alleles Freedom from genotyping. Lowering the entry barrier into this field Unrestricted access to strains, tissues, data, and statistical analysis suites (on-line mapping) Improved power and precision for trait mapping. Epistasis! Powerful new approaches to analysis of complex systems. Pleiotropy Analysis of gene-by-environment interactions A systems biology resource A new type of complex animal model to study common human diseases Broad utility: a resource that combines diverse haplotypes and that harbors a broad spectrum of alleles Freedom from genotyping. Lowering the entry barrier into this field Unrestricted access to strains, tissues, data, and statistical analysis suites (on-line mapping) Improved power and precision for trait mapping. Epistasis! Powerful new approaches to analysis of complex systems. Pleiotropy Analysis of gene-by-environment interactions A systems biology resource A new type of complex animal model to study common human diseases Design criteria for a Collaborative Cross

13. A set of 420 RI lines

14. Mapping with sequence data in hand

15. B6 and D2 haplotype contrast map of Chr 1

16. Celera SNP DB

17. ! ! Coincidence analysis

18. 1K Reference Population environment proteomics anatomy pathology anatomy pathology development epigenetic modifications cancer susceptibility transcriptome Meta- analysis metabolism endocrine profile immune response pathogens response pathogens pharmacokinetics physiology Integrative and cumulative analysis/synthesis

19. www.webqtl.org Phenotypes: from highly complex such as body size to highly specific, such as transcript expression difference QTL/QT gene Wilt Chamberlain: 7 feet 1 inch Willie Shoemaker: 4 feet 11 inches 1.44-fold 6 6 6 6 24th

20. Grin2b Cis QTL Trans QTL

21. Ret mRNA correlations in a small data set

22. Ret and Sh3d5

23. Ret GO analysis

24. Handdrawn sketch of the App neighborhood The App neighborhood

25. Associational Networks QTL networks add layer of shared causality

26. 1K Reference Population environment proteomics anatomy pathology anatomy pathology development epigenetic modifications cancer susceptibility transcriptome Meta- analysis metabolism endocrine profile immune response pathogens response pathogens pharmacokinetics physiology Integrative and cumulative analysis/synthesis

27. Per diem for 8,000 to 10,000 cages (~1500 K/year) Genotyping intermediate generations (~500 K/year) Prospective tissue harvesting and cryopreservation (~500 K/year) Molecular phenotyping of select tissue as proof-of- principle (500 K/year) Bioinformatics, statistical modeling, administration, colony management (~500 K/year) Cryopreservation of final lines at F25+ (~200 K) Sequencing of parental strains (unfunded) Per diem for 8,000 to 10,000 cages (~1500 K/year) Genotyping intermediate generations (~500 K/year) Prospective tissue harvesting and cryopreservation (~500 K/year) Molecular phenotyping of select tissue as proof-of- principle (500 K/year) Bioinformatics, statistical modeling, administration, colony management (~500 K/year) Cryopreservation of final lines at F25+ (~200 K) Sequencing of parental strains (unfunded) Cost Components: 24–28 M over 7–8 yrs

28. NIH Portfolio

29. Collaborators Ken Manly (UTHSC) David Threadgill (UNC Chapel Hill) Bob Hitzemann (OHSU) Gary Churchill (TJL) Fernando Pardo Manuel de Villena (UNC) Karl Broman (JHU) Dan Gaile (SUNY Buffalo) Kent Hunter (NCI) Jay Snoddy (ORNL) Jim Cheverud (Wash U) Tim Wiltshire (GNF) Ken Manly (UTHSC) David Threadgill (UNC Chapel Hill) Bob Hitzemann (OHSU) Gary Churchill (TJL) Fernando Pardo Manuel de Villena (UNC) Karl Broman (JHU) Dan Gaile (SUNY Buffalo) Kent Hunter (NCI) Jay Snoddy (ORNL) Jim Cheverud (Wash U) Tim Wiltshire (GNF) Lu Lu Elissa Chesler David Airey Siming Shou Jing Gu Yanhua Qu Lu Lu Elissa Chesler David Airey Siming Shou Jing Gu Yanhua Qu Supported by: NIAAA-INIA Program, NIMH, NIDA, and the National Science Foundation (P20-MH 62009), NEI, a Human Brain Project and the William and Dorothy Dunavant Endowment.