Complex trait analysis, develop-ment, and genomicsComplex trait analysis, develop-ment, and genomicsThe 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

“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.”

“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)

Elias Zerhouni: The NIH Roadmap. Science

302:63 (2003)

Material included in handouts

and on the CD also see www.complextrait.org

Material included in handouts

and on the CD also see www.complextrait.org

A group of ~150 mouse A group of ~150 mouse geneticists most of whom geneticists most of whom have interests in pervasive have interests in pervasive diseases and differences in diseases and differences in disease susceptibility. disease susceptibility.

General Aim: Improve General Aim: Improve resources for complex trait resources for complex trait analysis using mice.analysis using mice.Main catalysts and modelsMain catalysts and models

ENU mutagenesis programsENU mutagenesis programs

Sequencing and SNP consortia Sequencing and SNP consortia

•Catalyze genotyping of strainsCatalyze genotyping of strains•Simulation studies of crossesSimulation studies of crosses•Planning a collaborative crossPlanning a collaborative cross•Improved use of resourcesImproved use of resources

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 CTCThe short chronology of the CTC

Lusis et al. 2002: Genetic Basis of Common Human DiseaseLusis 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

Mixing mousegenomes (reluctantly)

Mixing mousegenomes (reluctantly)

Current practice: Keep it simple: high power with low n

Current practice: Keep it simple: high power with low n

Genetic dissectionGenetic 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.

Vp = Vg + VeVp = Vg + Ve

Vp = Vg + Ve + 2(Cov GE) + GXE + Vtech

Vp = Vg + Ve + 2(Cov GE) + GXE + Vtech

Standard recombinant inbred strains (RI)Standard recombinant inbred strains (RI)

C57BL/6J (B)C57BL/6J (B) DBA/2J (D)DBA/2J (D)

F1F1

20 generations

brother-sister

matings

20 generations

brother-sister

matings

BXD1BXD1 BXD2BXD2 BXD80BXD80+ … ++ … +

F2F2

BXD RIStrain setBXD RI

Strain set

fullyinbredfully

inbred

isogenicisogenic

hetero-geneoushetero-

geneous

Recombined chromosomes are

needed for mapping

Recombined chromosomes are

needed for mapping

femalefemale malemale

chromosome pairchromosome pair

InbredIsogenicsiblings

InbredIsogenicsiblings

BXDBXD

www.complextrait.orgwww.complextrait.org

Proposal for a Collaborative

Cross

Proposal for a Collaborative

Cross

1K Reference1K Reference

PopulationPopulationenvironmentenvironment

proteomicsproteomics

anatomypathologyanatomypathologydevelopmentdevelopment

epigeneticepigeneticmodificationsmodifications

cancercancersusceptibilitysusceptibility

transcriptometranscriptomeMeta-Meta-analysisanalysis

metabolismmetabolism

endocrine profileendocrine profile

immuneimmuneresponsepathogensresponsepathogens

pharmacokineticspharmacokinetics

physiologyphysiology

Integrative and cumulative analysis/synthesisIntegrative and cumulative analysis/synthesis

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 CrossDesign criteria for a Collaborative Cross

A set of 420 RI lines

A set of 420 RI lines

Mapping with sequence data in handMapping with sequence data in hand

B6 and D2 haplotype contrast map of Chr 1B6 and D2 haplotype contrast map of Chr 1

Celera SNP DBCelera SNP DB

!!

Coincidence analysisCoincidence analysis

1K Reference1K Reference

PopulationPopulationenvironmentenvironment

proteomicsproteomics

anatomypathologyanatomypathologydevelopmentdevelopment

epigeneticepigeneticmodificationsmodifications

cancercancersusceptibilitysusceptibility

transcriptometranscriptomeMeta-Meta-analysisanalysis

metabolismmetabolism

endocrine profileendocrine profile

immuneimmuneresponsepathogensresponsepathogens

pharmacokineticspharmacokinetics

physiologyphysiology

Integrative and cumulative analysis/synthesisIntegrative and cumulative analysis/synthesis

www.webqtl.orgwww.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 inchWillie Shoemaker: 4 feet 11 inches 1.44-fold

66

66

24th24th

Grin2bGrin2b

Cis QTLTrans QTL

Ret mRNA correlations in a small data set

Ret mRNA correlations in a small data set

Ret and Sh3d5Ret and Sh3d5

Ret GO analysis

Ret GO analysis

Handdrawn sketch of the App neighborhood

Handdrawn sketch of the App neighborhood

The App neighborhoodThe App neighborhood

Associational NetworksAssociational Networks72+++4@65D@ 4@105D@13@80D@@Taf1acChr 8 @ 120TATA box binding protein-associated factor, RNA polymerase I, C

71+4@100D@6@100D@Sart3Chr 5 @ 112Squamous cell carcinoma antigen recognized by T

cells 3

70++1@65B4@70D 6@100DDnmt1Chr 9 @21DNA methyltransferase 172+++1@65B 4@65D@ 13@90D@ 18@80B@Pak3bpChr 8 @12Pak3 binding protein89868669+++4@60D13@90DAA536646Chr 4 @1388570+4@100D 13@90D19@10BPrss15Chr 17@56Protease, serine 158370+++4@85D@ 6@100D11@85DAI573938Chr 1 @133EST73+++4@65D@@ 11D@80@ 13@90D Msh5Chr 17 @34amutS homolog 585848.8

5.99.87.6

10.59.29.47.69.58.59.97.99.26.9

10.08.5

68+3@10B4@20BGm2aChr 11 @56ganglioside M2 activator10.4

8.7

73+++4@65D@@13@90D@@Rps6ka4Chr 19 @3ribosomal protein S6

kinase 410.7

8.88383808372++1@65B4@60D 6@120DPkd1Chr 17@24Polycystic kidney disease 19.8

8.487858169+++4@55D 6@100D@9@65BAkt2Chr 7 @20v-akt murine thymoma viral

protooncogene 210.8

8.88568+6@95D 9@65B 12@85D X@15DCrhrChr 11 @105corticotropin releasing

hormone receptor9.37.6

8865+++2@135D@ 4@60D13@85DBlcapChr 2@158bladder cancer associated

protein10.4

8.4868471+++4@60D@@13@85D@Kifc2Chr 15@77kinesin family member C28.9

7.28971+++4@60D@@13@85D@@Kcnab2Chr 4@148potassium voltage-gated

channel, shaker related beta 2

8.97.2

8470+++4@60D@@9@60B X@45DUsp2Chr 9@44ubiquitin specific protease 211.3

9.98571+++4@60D@@13@85D@@AF100956Chr 17@3310.7

9.78971+++4@60D@@13@85D@@Hcn2Chr 10@80hyperpolarization-activated cyclic nuceotide-

gated pottasiumm 2

10.79.7

8872+++4@60D@ 9@60B11@80D 13@90DAkt1Chr 12@107thymona viral

protooncogene 111.010.1

8871+++4@65D 6@120DMntChr 11 @75Max binding protein (Rox)9.4

6.98969++4@100D 6@100D@7@75D 13@85D@Ccnd3Chr 17 @ 47cyclin D39.9

7.9818170++4@100D 6@115D@19@5BEdr1Chr 6 @ 123early development

regulator 19.97.9

81808067+4@105D9@40BTm7sf1Chr 13 @12transmembrane 7

superfamily member 19.58.1

858471++++4@80D5@115BtTie1Chr 4 @116tyrosine kinase receptor 110.0

8.682827975+9@40D@9@95D@Calm1Chr 12 @94calmodulin 113.6

12.5-80w71++4@65D13@85D@Brd4Chr 17 @31bromodomain 410.0

7.58771+++4@65D@ 13@85D18@80B@MtsskChr 4@114microtuble associated

testis specific serine/threonine kinase

10.07.5

8787848574+++4@65D 5@110B 6@25D 13@85D@@Prss25Chr 6@84Protease, serine 259.3

6.98370+++4@60D 13@90D@@ 19@50D X@10DIgfbp6Chr 15@103insulin like growth factor

binding protein 610.8

9.08370+++3@150D 4@65D 13@85D 19@402600002E23RikChr 4@1289.9

8.5908685 Peflin86848671+++4@60D@ 13@90D@ 19@35D@Chr 15@77cysteine and histidine rich

protein10.8

9.0Cyhr187Slc27a1 Fatp858377++9@40D@Prkar1aChr 11@110cAMP dependent

regulatory type 1 alpha13.412.1

9276+4@100B9@40D@Calm2Chr 17 @87calmodulin 215.4

13.29173++4@100B@ 6@130B 9@40D@Eef1a1Chr 9 @79eukaryotic translation elongation factor 1 alpha 114.813.0

957X++4@100B@ 6@15D@ 9@40D@Cox7cChr 11 @76cytochrome C oxidase

VIIc14.613.2

93ribosomal protein L4171++4@100B 8@75D@ 9@40D@ 14@15@Rpl41Chr 10@12915.5

13.59276+4@XXB@ 6@130B 9@40D@TrtChr 6 @101translationally regulated

transcript14.212.6

67+++6@30B@ 6@145B@ 9@50D@Rps23Chr 3@38ribosomal protein S2314.1

13.0909192899291 80+++9@40D@Snap25Chr 2@134synaptosomal associated

protein 25 kDa14.512.4

8581+++2@155D 9@40D 19@35BPrkcbChr 7@112protein kinase C beta13.0

11.793w84++++1@55B 9@40D 19@35B X@50BNckap1Chr 2@81NCK-associated protein 112.7

11.592W80++++19@45B X@65BSnap25Chr 9@25septin 712.8

10.591wW76++++12@80B 19@50B@Gria2Chr 3@81glutamate receptor

ionotropic AMPA 2 (GLUR2)

12.811.2

W81++++1@65B@ 12@30B12@80B@AI450991Chr 11@24KIAA0729 protein10.9

9.589wW81++++12@80B 19@45BTcf4Chr 18@70transcription factor 411.1

9.587wAll top 100 are +85wAll top 100 are +!W81+++1@65B@ 12@30B12@80B Dio2Chr 12@85deiodinase, iodothyronine

type 29.98.5

Sept791w72+-4@65B 5@115D 6@10D 9@40D4930415K17RikChr 18 @3610.4

9.3-87w74++PpiaChr 11 @6peptidylprolyl isomerase

A14.813.2

4@100B 6@120B9@40D 9473+-4@50B 6@10D@ 8@75D 9@40D@Rpl7Chr 14@20ribosomal protein L714.4

12.7

73+4@55B@ 6@10D@ 6@120B 9@40DRpl30Chr 11@50ribosomal protein L3013.7

12.6909390885@115B 6@120D 9@40B8379-81-8871+-Cbfa2t3hChr 8 @123core binding factor, runt

domain, alpha 2 translocated to 3 homolog

8.86.8

4@100D 5@100B 9@75B 12@25B 88949570+-Gpaa1Chr 15@77cGPI anchor attachment

protein 110.4

7.44@100D@ 6@100D@ 8184948986w86w89w88w70+-6@120D@Chr 5@39heparan sulfate 3-O-

sulfotransferase 18.56.6

Hs3st1-79w-79w968674++2@125D@ 8@75D 9@45D 11@110DAppChr 16 @8614.1

13.0

amyloid beta precursor protein829371+++2@125D 4@100B

8@70D 11@100D ApoeChr 7@1514.8

13.2

apolipoprotein E8874+++2@120D 4@100B 8@70D 11@100D@ Atp6lChr 17@2314.5

13.29390757774+++4@60D@ 6@100D 13@95D X@15D@Scamp3Chr 3 @9010.4

8.7

secretory carrier membrane protein 3-7479-81w68+-1@175D 4@65BChr 12@39Dnaj homolog subfamiy

B911.010.1

Dnajb97759+-2@5B 4@140B 5@95B 9@60BtChr 9@509.7

8.7Drd266+-2@5D 3@50D 4@140D 9@65@10@35D 12@100B 15@10D X@5B

Chr 10@4210.49.4

AU04429069+-8@35D 9@55BChr 4@109.68.3

0610010I23Rik7456+-4@115D@ 4@140D@ 5@95D 9@100D

Chr 13@5512.710.5

C85523-7361+-4@10D 5@90B 9@60B 17@55D

Chr 15@8111.911.2

Cbx672+-4@10D@ 4@60D 5@95B 9@45B

Chr 12@1711.510.4

Ntsr27373neurotensin receptor 277+-9@60B 12@100D@ 19@50D@ X@60@Chr 11@10311.2

10.2AW12413373+++9@65D@@ 12@65B@ 17@55B

Chr 16@119.98.8

C7643965+-2@5B 9@45@ 9@65@ X@10D

Chr 11@1029.98.5

Ramp269-6969Crip2797371+++4@60D@@13@85D@@Kcnab2Chr 4@148potassium voltage-gated

channel, shaker related beta 2

8.97.2

71+++4@60D@@13@85D@@Hcn2Chr 10@80hyperpolarization-activated cyclic nuceotide-

gated pottasiumm 2

10.79.7

75-77XX+-4@XXD@ 4@60D 5@95B 9@45B

Chr 15@129.78.2

Rpo2tc1RNA polymerase II transcriptional coactivator 1-79XX+-4@XXD@ 4@60D 5@95B 9@45B

Chr 12@199.X8.2

Taf1bTATA box binding protein associated factor, RNA

polymerase I, B

-7881chromobox homolog 6726X+-4@XX 5@90B 9@60B 17@55D

Chr 11@20XX11.2

Slc1a4solute carrier family 1 glutamate/neurtal amino

acid transporter 4

7371hippocampus 38.5 kDa8372+-4@10D 4@45D 19@45D X@80D

Chr 11@11611.210.1

Slc9a3r1sodium/hydrogen exchanger isoform 3

regulator 1

86XX+-4@XXD 5@90B 9@60B 17@55D

Chr 4@1381X.911.2

Casp9caspase 9 ?AI115399

86++++9@65D@ 12@95BChr 1@1710.48.3

Tceb1transcription elongation factor B 184807663+-1@95B 5@50B@

12@45B@Chr 8@467.5

6.5Casp3caspase 3, apoptosis related cysteine protease-69-72xx8872+++4@60D@ 9@60B

11@80D 13@90DAkt1Chr 12@10711.0

10.188-81w4@60D@ 6@100D 13@95D X@15D@Scamp3Chr 3 @9010.4

8.779dopamine receptor D2receptor activity modifying

protein 2cysteine rich protein 2 thymona viral

protooncogene 1secretory carrier

membrane protein 3Ethanol-induced conditioned place preference

742@5B 4@100B@ 7@95B 8@75@ 18@15D@759190909256+ –1@155D@ 1@175DPsen2Chr 1@1829.0

7.7

presenilin 2-74-70-7359– –4@110D 6@155D@ 11@120B@ 18@70B@EspChr 1@1368.4

6.7

embryonic stem cell phosphatase7778+++9@95D@Ephb6Chr 6@4210.9

9.088-82 Eph receptor B6-8578+++6@120B 9@95DTcea2Chr 2@18010.9

9.0

transcription elongation factor A (SII), 29377+++9@120DPcgChr 12@10811.3

10.0

psoriasis candidate gene959378+++4@110B, 9@120D 14@55D 18@60DCol1a2Chr 6@411.8

10.5

procollagen type I, alpha 295899068+–1@65B4@60D 6@120DR75078Chr 15@759.8

8.4

72+–4@100D 9@95B@@ 11@10D 13@85D AA408674Chr 17@279.1

7.8

74++6@120B 9@45DZwintChr 10 @7314.713.0

8672++1@135D@ 4@110B@ 8@85D@Tuba6Chr 12@115tubulin alpha 614.8

13.5928073++2@125D@ 6@10D 9@45D 11@110DHsp84-1Chr 17@4514.0

12.8

heat shock protein, 84 KDa 195guanine nucleotide binding

protein alpha stimulating9072++1@XX@ 4@110B@ 8@85D@Tuba2Chr 15@100tubulin alpha 21X.8

13.5898989898469++9@50D@ 14@15DUbcChr 15@100ubiquitin C14.1

13.1848772+++2@120D 4@100B 6@120B 9@40D UbbChr 11@6315.5

13.9

ubiquitin B919072+++2@120D@ GnasChr 2@17514.913.9

929396Arf113.712.8

71++8@85D 14@5D Chr 11@60ADP-ribosylation factor87ZW10 interacting protein 1ATPase, H+ transporting, lysosomalChr 2 @ 120 MbChr 19 @ 40 MbChr 12 @ 35 Mb88wChr 9 @ 40 MbChr 8 @ 85 Mb

73+–7@85D 9@95B 13@100D Hsf1Chr 15@779.2

7.9

Heat shock factor 1

Chr 4 @ 60 MbChr 4 @ 100 MbChr 9 @ 100 MbChr 13 @ 85 MbChr 2 @ 5 MbChr 9 @ 65 MbChr 4 @ 60 Mb

QTL networks add layer of shared causality

QTL networks add layer of shared causality

1K Reference1K Reference

PopulationPopulationenvironmentenvironment

proteomicsproteomics

anatomypathologyanatomypathologydevelopmentdevelopment

epigeneticepigeneticmodificationsmodifications

cancercancersusceptibilitysusceptibility

transcriptometranscriptomeMeta-Meta-analysisanalysis

metabolismmetabolism

endocrine profileendocrine profile

immuneimmuneresponsepathogensresponsepathogens

pharmacokineticspharmacokinetics

physiologyphysiology

Integrative and cumulative analysis/synthesisIntegrative and cumulative analysis/synthesis

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 yrsCost Components: 24–28 M over 7–8 yrs

NIH PortfolioNIH Portfolio

CollaboratorsCollaboratorsKen 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.

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.