Html Karl W Broman Department of Biostatistics Johns Hopkins University
Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of...
-
Upload
hassan-ohara -
Category
Documents
-
view
216 -
download
0
Transcript of Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of...
![Page 1: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/1.jpg)
Karl W Broman
Department of BiostatisticsJohns Hopkins University
http://www.biostat.jhsph.edu/~kbroman
The genetic dissectionof complex traits
![Page 2: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/2.jpg)
2
Goal
Identify genes that contribute to complex human diseases
Complex disease = one that’s hard to figure out
Many genes + environment + other
QTL = quantitative trait locus
Genomic region that affects a quantitative trait
![Page 3: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/3.jpg)
3
The genetic approach
• Start with the trait; find genes the influence it.
– Allelic differences at the genes result in phenotypic differences.
• Value: Need not know anything in advance.
• Goal
– Understanding the disease etiology (e.g., pathways)
– Identify possible drug targets
![Page 4: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/4.jpg)
4
Approaches
• Experimental crosses in model organisms
• Mutagenesis in model organisms
• Linkage analysis in human pedigrees
– A few large pedigrees
– Many small families (e.g., sibling pairs)
• Association analysis in human populations
– Isolated populations vs. outbred populations
– Candidate genes vs. whole genome
![Page 5: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/5.jpg)
5
Inbred mice
![Page 6: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/6.jpg)
6
Advantages of the mouse
• Small and cheap
• Inbred lines
• Disease has simpler genetic architecture
• Controlled environment
• Large, controlled crosses
• Experimental interventions
• Knock-outs and knock-ins
![Page 7: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/7.jpg)
7
Disadvantages of the mouse
• Is the model really at all like the corresponding human disease?
• Still not as small (or as fast at breeding) as a fly.
![Page 8: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/8.jpg)
8
The mouse as a model
• Same genes?
– The genes involved in a phenotype in the mouse may also be involved in similar phenotypes in the human.
• Similar complexity?
– The complexity of the etiology underlying a mouse phenotype provides some indication of the complexity of similar human phenotypes.
• Transfer of statistical methods.
– The statistical methods developed for gene mapping in the mouse serve as a basis for similar methods applicable in direct human studies.
![Page 9: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/9.jpg)
9
Mutagenesis
Advantages
+ Can find things
+ Genes at least indicate a pathway
Disadvantages
– Need cheap phenotype screen
– Mutations must have large effect
– Genes found may not be relevant
– Still need to map the mutation
– Mutations with recessive effects are hard to see
![Page 10: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/10.jpg)
10
The intercross
![Page 11: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/11.jpg)
11
The data
• Phenotypes, yi
• Genotypes, xij = AA/AB/BB, at genetic markers
• A genetic map, giving the locations of the markers.
![Page 12: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/12.jpg)
12
Phenotypes
133 females
(NOD B6) (NOD B6)
![Page 13: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/13.jpg)
13
NOD
![Page 14: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/14.jpg)
14
C57BL/6
![Page 15: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/15.jpg)
15
Agouti coat
![Page 16: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/16.jpg)
16
Genetic map
![Page 17: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/17.jpg)
17
Genotype data
![Page 18: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/18.jpg)
18
Statistical structure
• Missing data: markers QTL
• Model selection: genotypes phenotype
![Page 19: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/19.jpg)
19
The simplest method
“Marker regression”
• Consider a single marker
• Split mice into groups according to their genotype at a marker
• Do an ANOVA (or t-test)
• Repeat for each marker
![Page 20: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/20.jpg)
20
LOD curves
![Page 21: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/21.jpg)
21
Chr 9 and 11
![Page 22: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/22.jpg)
22
Epistasis
![Page 23: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/23.jpg)
23
Back to the strategy
• First: QTL mapping results in a 10-20 cM region
• Next step: create congenics
• Then: subcongenics
• Then: test candidates
• Finally: prove a gene is the gene
![Page 24: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/24.jpg)
24
• Recombinant inbred lines (RILs)
• Advanced intercross lines (AILs)
• Heterogeneous stock (HS)
• The Collaborative Cross (CC)
• Partial advanced intercross (PAI)
• Association mapping across mouse strains
• Combining crosses, accounting for the history of the inbred strains
• Gene expression microarrays
“Modern” approaches
![Page 25: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/25.jpg)
25
Recombinant inbred lines
![Page 26: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/26.jpg)
26
RI lines
Advantages
• Each strain is a eternal resource.
– Only need to genotype once.
– Reduce individual variation by phenotyping multiple individuals from each strain.
– Study multiple phenotypes on the same genotype.
• Greater mapping precision.
Disadvantages
• Time and expense.
• Available panels are generally too small (10-30 lines).
• Can learn only about 2 particular alleles.
• All individuals homozygous.
![Page 27: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/27.jpg)
27
The RIX design
![Page 28: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/28.jpg)
28
The “Collaborative Cross”
![Page 29: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/29.jpg)
29
Genome of an 8-way RI
![Page 30: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/30.jpg)
30
Heterogeneous stock
McClearn et al. (1970)
Mott et al. (2000); Mott and Flint (2002)
• Start with 8 inbred strains.
• Randomly breed 40 pairs.
• Repeat the random breeding of 40 pairs for each of ~60 generations (30 years).
• The genealogy (and protocol) is not completely known.
Note: AILs are similar, but start with 2 strains and don’t go as many generations
![Page 31: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/31.jpg)
31
Heterogeneous stock
![Page 32: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/32.jpg)
32
• Recombinant inbred lines (RILs)
• Advanced intercross lines (AILs)
• Heterogeneous stock (HS)
• The Collaborative Cross (CC)
• Partial advanced intercross (PAI)
• Association mapping across mouse strains
• Combining crosses, accounting for the history of the inbred strains
“Modern” approaches
![Page 33: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/33.jpg)
33
Towards proof
• Gene has nonsynonymous mutation
• Gene shows difference in expression between parental strains
• Expression variation correlated with QTL genotype
• RNA interference
• Knock out/knock in
![Page 34: Karl W Broman Department of Biostatistics Johns Hopkins University kbroman The genetic dissection of complex traits.](https://reader035.fdocuments.in/reader035/viewer/2022062511/5519ce5955034649768b47e0/html5/thumbnails/34.jpg)
34
Summary
• Experimental crosses in model organisms+ Cheap, fast, powerful, can do direct experiments– The model may relevant to the human disease
• Standard QTL mapping results in large regions with many genes
• Fine mapping– Congenics, AILs, RILs, HS, PAI, association mapping– Expression differences
• Proof– RNA interference– Knock outs/knock ins