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Using mouse genetics to understand human disease

发布时间:2013-12-14 15:01:28  

Mark Daly

Whitehead/Pfizer

Computational Biology

Fellow

What we do

?Genetics: the study of the inheritance of

biological phenotype

–Mendel recognized discrete units of inheritance–Theories rediscovered and disputed ca. 1900–Experiments on mouse coat color proved

Mendel correct and generalizable to mammals–We now recognize this inheritance as being

carried by variation in DNA

Why mice?

?Mammals, much better biological model

?Easy to breed, feed, and house

?Can acclimatize to human touch

?Most important: we can experiment in many ways not possible in

humans

Mice are close to humans

Mouse sequence reveals great

similarity with the human genomeExtremely high conservation: 560,000 “anchors”

Mouse-Human Comparison

both genomes 2.5-3 billion bp long

> 99% of genes have homologs

> 95% of genome “syntenic”

Genomes are rearranged copies

of each other

Roughly 50% of bases change in the evolutionary time from mouse to human

Mouse sequence reveals great

similarity with the human genomeExtremely high conservation: 560,000 “anchors”

Anchors (hundreds of bases with >90% identity)represent areas of evolutionary selection…

…but only 30-40% of the highly conserved

segments correspond to exons of genes!!!

What we can do?Directed matings

?Inbred lines and crosses?Knockouts

?Transgenics

?Mutagenesis

?Nuclear transfer?Control exposure to

pathogens, drugs, diet, etc.

Example: diabetes related miceavailable from The Jackson LabsType I diabetes (3)

Type II diabetes (3)

Hyperglycemic (27)

Hyperinsulinemic (25)

Hypoglycemic (1)

Hypoinsulinemic (5)

Insulin resistant (30)Impaired insulin processing (7)Impaired wound healing (13)?????????

Inbreeding

?Repeated brother-sister mating leads to completely

homozygous genome –no variation!

Experimental Crosses

?Breed two distinct inbred lines

?Offspring (F1) are all genetically identical –they each have one copy of each chromosome from each parent

?Further crosses involving F1 lead to mice with unique combinations of the two original strains

Experimental Cross

Experimental Cross: backcross?F1 bred back to one of

the parents

Backcross (F1 x RED)

offspring:

50% red-red50% red-blue?

Experimental Cross: F2 intercross?One F1 bred to

another F1

?F2 intercross (F1xF1)

offspring:

25% red-red

50% red-blue25% blue-blueF2

Trait mappingF2

Trait mapping

Blue trees = tall, Red trees = short

In the F2 generation, short trees tend to carry “red” chromosomes where theheight genes are located, taller trees tend to carry “blue” chromosomes QTL mapping use statistical methods to find these regions

How do we distinguish

chromosomes from different strains??Polymorphic DNA markers such as Single Nucleotide Polymorphisms (SNPs) can be used to distinguish the parental origin of offspring chromosomes

Example: susceptibility to TbC3H mice extremely susceptible to TbB6 mice resistantF1, F2 show intermediate levels of susceptibility???

One gene location already known

?

?

Previous work identified chromosome 1 as carrying a major susceptibility factorCongenic C3H animals carrying a B6 chromosome 1 segment were bred

Congenic and consomic mice?Derived strains of mice in which the

homozygous genome of one mouse strain has a chromosome or part of a chromosome substituted from another strain

C3H B6 C3H.B6_chr1

Chr 1

Chr 2

Chr 3

Chr 4

Etc.

Tb mapping cross

F2 intercross:

C3H.B6-

sst1x

xB6C3H.B6-sst1-MTB-susceptible, carrying B6 chr 1 resistanceF1B6-MTB-resistant

Trait–survival following

Results: 3 new gene locations

identified!

Gene identified on chromosome 12

100

lav

ivr

us50

%

A.At the end of chr 12 –mice

Mouse History

?Modern

“house mice” emerged from Asia into the fertile crescent as agriculture was born

Mouse history

Recent mouse history

Fancy mouse breeding -Asia, Europe

(last few centuries)

Retired schoolteacher Abbie Lathrop

collects and breeds these mice

Granby, MA –1900

Castle, Little and

others form most

commonly used

inbred strains

from Lathrop stock(1908 on)

W.E. Castle C.C. Little

Mouse history

Mouse history

?Asian musculusand European domesticusmice dominate the world but have evolved separately over ~ 1 Million years

?Mixing in Abbie Lathrop’s schoolhouse created all our commonly used mice from these two distinct founder groups

Genetic Background of the

C57BL/6

C3H

DBAinbred lab miceAvg segment size ~ 2 Mb

Comparing two inbred strains –frequency of differences in 50 kb segments

{<1 SNP/10 kb~40 SNP/10 kb{

Finding the genes responsible for

biomedical phenotypes

C3H (susceptible)

B6 (resistant)Traditionally: positional cloning is painful

(e.g., generating thousands of mice for fine mapping, breeding congenics) –As a result, countless significant QTLs have been identified in mappingcrosses but only a small handful have thusfar resulted in identificationof which gene is responsible –the critical information that will advanceresearch into prevention and treatment!

Using DNA patterns to find genes

C3H (susc.)

B6 (res.)

Critical Region

Using DNA patterns to find genes

C3H (susc.)

B6 (res.)

DBA (susc.)

Critical Region

Example: mapping of albinism

Critical region

First genomic region mapped

129S1AKR

TA

AG

*T

CT

CT

CA

*A

CT

GG

GG

TT

AA

CC

GG

AA

GG

GG

GG

A_JBALB_cC3HC57B6

ATAA

GAGG

T*TT

TCTT

TCTT

ACAA

AGAA

TCTT

GGGC

GGGT

TTTA

AAAG

CCCT

GGGA

AAAC

GGGC

GGGC

GGGA

CBADBA2FVB

AAA

GGG

TTT

TTT

TTT

AAA

AAA

TTT

CCC

TTT

AAA

GGG

TTT

AAA

CCC

CCC

CCC

AAA

INODNZBSJLSWR

AA*AA

GGAGG

TTCTT

TTCTT

TTCTT

AACAA

AA*AA

TTCTT

GGCCC

GGTTT

TT*AA

AAGGG

CCTTT

GGAAA

AACCC

GGCCC

GGCCC

GGAAA

Chr 4 35.7 37.6 37.9 39.4

(Mb)

Future Genetic Studies

Thanks to

(Whitehead Institute)Claire Wade

Andrew Kirby

(MIT Genome Center)EJ KulbokasMike Zody

Eric Lander

Kerstin Lindblad-TohFunding:

Whitehead InstitutePfizer, Inc.

National Human Genome Research Institute

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