Experimental crosses

Inbred Strain Cross

Backcross

F2 cross

F2

F1

F0

Generation

0

200

400

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800

1000

1200

1400

0.5

Phen

otyp

e

ABAA BB

Experimental crossesInbred strain crossesRecombinant inbredsAlternatives

Recombinant InbredsF0 Parental Generation

F1 Generation

F2 Generation

Interbreeding for approximately 20 generations to produce recombinant inbreds

Experimental crossesInbred strain crossesRecombinant inbredsAlternatives

Three problems in QTL analysis

Missing genotype problemSignificance thresholdsModel selection problem

Missing genotype problem

M1 M2 M3 Q M4 M5H A A - A AH H H - A AB B - - H H

Key referencesMaximum likelihood methods

Linear regression

Imputation

r/qtl

http://www.rqtl.org/Broman, Sen & Churchill

Significance Thresholds

Significance Thresholds

Suggestive Significant Mapping method P LOD P LOD Backcross 3.40E-03 1.9 1.00E-04 3.3 Intercross (2 df) 1.60E-03 2.8 5.20E-05 4.3

Lander, E. Kruglyak, L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results Nature Genetics. 11, 241-7, 1995

ThresholdsPermutation test

ThresholdsPermutation test SUBJECT.NAME Sex Phenotype m1 m2 m3 m4 F2$798 F -0.738004 -1 1 1 -1 F2$364 F 0.413330 0 0 0 0 F2$367 F 1.417480 -1 1 1 -1 F2$287 F 0.811208 1 -1 -1 1 F2$205 M 1.198270 0 0 0 0

ThresholdsPermutation test SUBJECT.NAME Sex Phenotype m1 m2 m3 m4 F2$798 F -0.738004 -1 1 1 -1 F2$364 F 0.413330 0 0 0 0 F2$367 F 1.417480 -1 1 1 -1 F2$287 F 0.811208 1 -1 -1 1 F2$205 M 1.198270 0 0 0 0

SUBJECT.NAME Sex Phenotype m1 m2 m3 m4 F2$798 F 0.413330 -1 1 1 -1 F2$364 F 1.417480 0 0 0 0 F2$367 F 1.198270 -1 1 1 -1 F2$287 F -0.738004 1 -1 -1 1 F2$205 M 0.811208 0 0 0 0

shuffle

Permutation tests to establish thresholds

Empirical threshold values for quantitative trait mappingGA Churchill and RW Doerge

Genetics, 138, 963-971 1994

An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand.

The model problem

The model problemLinked QTL corrupt the position estimatesUnlinked QTL decreases the power of QTL detection

Alternative resources

0

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30

0 10 20 30 40 50 60 70 80 90 100Distance cM

LOD

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0 10 20 30 40 50 60 70 80 90 100Distance cM

LOD

One locus may contain many QTL

Genetically Heterogeneous Mice

Pseudo-random matingfor 50 generations

Heterogeneous Stock F2 Intercross

x

Avg. Distance Between Recombinations:

F1

F2HS~2 cM

F2 intercross~30 cM

Pseudo-random matingfor 50 generations

Heterogeneous Stock F2 Intercross

x

Avg. Distance Between Recombinations:

F1

F2HS~2 cM

F2 intercross~30 cM

Hidden Chromosome Structure

Observed chromosome structure

Multipoint method (HAPPY) calculates the probability that an allele descends from a founder

using multiple markers

single marker association

single marker associationHAPPY method

Many peaks

mean red cell volume

Linkage disequilibrium

Mouse F2 population:

LD on chromosome 1

A/J AKR/J BALB/cJ C3H/HeJ C57BL/6J CBA/J DBA/2J LP/J

Mouse Heterogenenous Stock: LD on chromosome 11

Mapping in structured populations by resample model averaging.Valdar W, Holmes CC, Mott R, Flint J.Genetics. 2009 Aug;182(4):1263-77.

Efficient control of population structure in model organism association mapping.Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E. Genetics. 2008 Mar;178(3):1709-23.

LD on chromosome 11 in three outbred stocks

LD on chromosome 11 in three outbred stocks

Imputation of genomes

SleepVocalization

Dissection16 weeks 21 weeks

HypoxiaEcho/ECG

Basal ActivityStartle PPIFear ConditioningSwim test

Elevated Plus MazeOpen Field TestNeophagia

Crl:CFW(SW)

DNABrainBloodSpleenLimbsTail fibroblastsEarsLiverAdrenalsLungsHeart

x 2000

Phenotyping pipeline

FACS:CD4/CD8 ratio

H2-Ea

Scarb1

Biochemistry:Total Cholesterol