Post on 05-Jan-2016
description
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.