from qtl to qtg: are we getting closer? sagiv shifman and ariel darvasi the hebrew university of...
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From QTL to QTG: Are we getting closer?
Sagiv Shifman and Ariel Darvasi
The Hebrew University of JerusalemThe Hebrew University of Jerusalem
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Presentation OutlinePresentation Outline
Overview of fine QTL mapping strategiesOverview of fine QTL mapping strategies
Inbred strain sequence/haplotype information for Inbred strain sequence/haplotype information for fine QTL mappingfine QTL mapping
Yin-Yang crosses: A framework for applying inbred Yin-Yang crosses: A framework for applying inbred strain sequence/haplotype information to fine map strain sequence/haplotype information to fine map QTLsQTLs
Simulation analysis using Celera’s sequence Simulation analysis using Celera’s sequence information of 4 inbred strains (C57, A/J, DBA, 129)information of 4 inbred strains (C57, A/J, DBA, 129)
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The DifficultiesThe Difficulties
GeneticsGenetics Genotype/phenotype correlationGenotype/phenotype correlation RecombinationRecombination
FunctionalFunctional The “end-game” (knockout, transgenic, The “end-game” (knockout, transgenic,
mutation analysis, RNAi, etc.)mutation analysis, RNAi, etc.)
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Fine Mapping StrategiesFine Mapping Strategies
Genomewide-based strategies:Genomewide-based strategies: Large scale BC, F2, half sibs, etc.Large scale BC, F2, half sibs, etc. Advanced Intercross Lines (AIL)Advanced Intercross Lines (AIL) The heterogeneous stock (HS)The heterogeneous stock (HS)
Locus-based strategies:Locus-based strategies: Selective phenotypingSelective phenotyping Recombinant progeny testingRecombinant progeny testing Interval specific congenic strains (ISCS)Interval specific congenic strains (ISCS) Recombinant inbred segregation test (RIST)Recombinant inbred segregation test (RIST)
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Sample size requiredSample size required
Experimental Experimental designdesign
N for N for detectiondetection
N for mapping N for mapping into 1cMinto 1cM
FF221001006,0006,000
BCBC10010010,00010,000
RI StrainsRI Strains4040500500
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Advanced intercross lines (AIL)Advanced intercross lines (AIL)
Semi-random intercrossing
P F1 F2 F3 Ft
CI = CICI = CIF2 F2 / (t/2)/ (t/2)
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AIL - experimental resultsAIL - experimental results
HDL – QTLWang et al. 2003
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The heterogeneous stock (HS)The heterogeneous stock (HS)
Eight-way cross of:
C57BL/6, BALB/C, RIII, AKR, DBA/2, I, A/J C3H
Established 30 years ago (~60 generations)by
McClearn et al.
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HS - Experimental resultsHS - Experimental results
Open field activity
Talbot et al. 1999
0 0.2 0.4 0.6 0.8 1.0 1.2 1.40 0.2 0.4 0.6 0.8 1.0 1.2 1.4
cMcM
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Locus-based strategies:Selective phenotyping (SPh)Selective phenotyping (SPh)
Theoretical basis: Only recombinants
increase mapping accuracy for a
detected QTL.
Procedure: Only individuals
recombinant at a QTL-containing
interval are subsequently phenotyped.
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SPh - Experimental resultsSPh - Experimental results
0
2
4
6
0 20 40 60 80cM
LO
D
Lesions density
Paigen et al. BC
SPh-BC
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Recombinant progeny Recombinant progeny testingtesting
QTLQTL
Males, recombinant at an interval of interest, are progeny tested to check which QTL allele was retained.
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Interval specific congenic strains Interval specific congenic strains (ISCS)(ISCS)
QTLQTL
ISCS ISCS are produced by a series of backcrosses and intercrosses
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Recombinant inbred segregation Recombinant inbred segregation test (RIST)test (RIST)
P1 RI P2
x x
F1,1 F1,2
F2,1 F2,2
QTLQTL
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RIST - Experimental resultsRIST - Experimental results
F21 F22
C57L AKRAKXL-16
P=0.41
D2MIT64
D2MIT200
P=0.02
B. TaylorA. Darvasi
Obesity QTLObesity QTL
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In silico mapping of complex disease-related traits in mice
Grupe et al. 2001
Comment:
Chesler et al. 2001Darvasi 2001
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Park et al. 2003
Wiltshire et al. 2003
Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse
Multiple Cross and Inbred Strain Haplotype Mapping of Complex-Trait Candidate Genes
Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice
Yalcin et al. 2004
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QTL detection with two inbred lines (P1 and QTL detection with two inbred lines (P1 and P2) P2) ↓↓
Estimating QTL map locationEstimating QTL map location↓↓
Sequence based fine mappingSequence based fine mapping↓↓
Selecting an optimal new inbred strain (Pi)Selecting an optimal new inbred strain (Pi)↓↓
Yin-Yang crossesYin-Yang crosses
Yin-Yang Crosses : A framework for Yin-Yang Crosses : A framework for Multiple Cross Inbred Strain Haplotype Multiple Cross Inbred Strain Haplotype
Mapping Mapping
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QTL mapped in a AxB crossQTL mapped in a AxB cross
A B
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Sequence/Haplotype Sequence/Haplotype InformationInformation
A B
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Yin-Yang CrossesYin-Yang Crosses
A B
C
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Simulation AnalysisSimulation Analysis
Initial cross between A/JxC57Initial cross between A/JxC57
22,814 SNPs, each at its turn, simulated as the QTN22,814 SNPs, each at its turn, simulated as the QTN
The strain closest to being half similar to A/J and half to C57 The strain closest to being half similar to A/J and half to C57 was selected first for Yin-Yang crosses (DBA or 129)was selected first for Yin-Yang crosses (DBA or 129)
The forth strain was subsequently introducedThe forth strain was subsequently introduced
At each stage the number of the remaining SNPs that can At each stage the number of the remaining SNPs that can be the QTN, and the size of the QTL containing interval be the QTN, and the size of the QTL containing interval were estimatedwere estimated
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Mapping Resolution: Chromosome Mapping Resolution: Chromosome 16 16
2 strains3 strains4 strains
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Low resolution region
High resolution region
11 12 13 14 15
0.0
00
.02
0.0
40
.06
Number of SNPs = 30 Interval= 2.1 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
11 12 13 14 15
0.0
00
.05
0.1
00
.15
Number of SNPs = 12 Interval= 1 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
11 12 13 14 15
0.0
0.1
0.2
0.3
0.4
Number of SNPs = 5 Interval= 0.4 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
57 58 59 60 61
0.0
00
.02
0.0
4
Number of SNPs = 2318 Interval= 4 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
57 58 59 60 61
0.0
00
.02
0.0
40
.06
Number of SNPs = 1696 Interval= 3.6 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
57 58 59 60 61
0.0
00
.02
0.0
40
.06
Number of SNPs = 1696 Interval= 3.6 Mb
Location (Mb)
pro
po
rtio
n o
f S
NP
s
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Mean Reduction in Interval Mean Reduction in Interval Length Length
23
4
5
2
1
54%51%
37%44%
42%
30% 31%30%
21%
Number of Strains
Initial Lentgh (Mb)
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Distribution of Mapping Resolution with 4 Inbred Distribution of Mapping Resolution with 4 Inbred Strains Strains
Pro
port
ion0 1 2 3 4 50
.00
0.0
40
.08
0 1 2 3 4 50.0
00
.10
0 1 2 3 4 50.0
00
.10
0.2
0
Interval length
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ConclusionsConclusions Using inbred strain sequence/haplotype information Using inbred strain sequence/haplotype information
combined with multiple crosses (Yin-Yang crosses) can combined with multiple crosses (Yin-Yang crosses) can efficiently aid QTL fine mapping efficiently aid QTL fine mapping
With 4 strains most regions exhibit modest mapping With 4 strains most regions exhibit modest mapping resolution. resolution.
The significant haplotype variation observed in 4 strains The significant haplotype variation observed in 4 strains may suggest that with a large number of strains in hand may suggest that with a large number of strains in hand significant resolution can be achieved.significant resolution can be achieved.
With sequence information in hand, resolution maps and algorithms With sequence information in hand, resolution maps and algorithms can be established to guide the researchers to the optimal strain can be established to guide the researchers to the optimal strain selection strategy and provide the resolution expected for their selection strategy and provide the resolution expected for their region of interest.region of interest.
A large number of sequenced strains will allow the actual selection A large number of sequenced strains will allow the actual selection of a very small number of strains for additional crosses.of a very small number of strains for additional crosses.
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So, Do We Need the 1K RI So, Do We Need the 1K RI Set?Set?
YESUntil we have the 1K RI set any QTL mapping strategy is like riding a bike: it’s fun and we can get very far – Once we get something with an engine though, we will feel the difference!
… we are still missing an engine for the “end-game” – Genetics is not everything