Accelerating positional cloning in mice using ancestral haplotype patterns
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Accelerating positional cloning in mice using ancestral haplotype patterns. Mark Daly Whitehead Institute for Biomedical Research. Kerstin Lindblad-Toh Whitehead/MIT Center for Genome Research. Mouse sequence reveals great similarity with the human genome.

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Accelerating positional cloning in mice using ancestral haplotype patterns

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Accelerating positional cloning in mice using ancestral haplotype patterns

Accelerating positional cloning in miceusing ancestral haplotype patterns

Mark Daly

Whitehead

Institute for

Biomedical Research


Accelerating positional cloning in mice using ancestral haplotype patterns

Kerstin Lindblad-Toh

Whitehead/MIT Center for Genome Research


Mouse sequence reveals great similarity with the human genome

Mouse sequence reveals great similarity with the human genome

Extremely high conservation: 560,000 “anchors”

Mouse-Human Comparisonboth genomes 2.5-3 billion bp long

> 99% of genes have homologs

> 95% of genome “syntenic”


Mouse history

Mouse history

Mouse Genetics, L. Silver


Recent 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


Critical components of inbred strain diversity

Critical components of inbred strain diversity

  • Asian musculus and European domesticus mice dominate the world but have evolved separately over ~ 1 Million years

  • Thousands of years of fancy mouse breeding resulted in highly homogeneous versions of these wild mice being traded and ending up in Lathrop’s schoolhouse


Structure of variation in the laboratory mouse

Structure of variation in the laboratory mouse

  • Study 1: compare finished BACs from strain 129 to recent C57BL/6J genome assembly

  • Study 2: extrapolate general observations utilizing WGS reads from 129, C3H, Balb/c done as part of the MGSC


Distribution of variation rates 70 unlinked 50 kb segments 129 vs b6

Distribution of variation rates 70 unlinked 50 kb segments (129 vs. B6)

{

{

<1 SNP/10 kb

~40 SNP/10 kb


Distribution of variation rates 70 unlinked 50 kb segments

Distribution of variation rates 70 unlinked 50 kb segments

{

{

Only 1/3 validate

~99% validate


Low and high snp rate suggest recent and distant ancestry

Low and High SNP rate suggest recent and distant ancestry


Snp discovery analysis summary

SNP discovery analysis summary

  • Comparisons of 129 and C57BL/6 show alternating regions of high SNP density (~1 per 200-250 bp) and low SNP density (~1 per 20,000 bp)

  • Genome-wide shotgun suggests these segments average 1 Mb

  • C3H and Balb/c comparisons to C57BL/6 give identical picture with regions of divergence and identity varying


Genetic background of the inbred lab mice

Genetic Background of the inbred lab mice

C57BL/6

musc

domest

musc

C3H

domest

musc

domest

{

DBA

domest

cast

domest

musc

Avg segment size ~ 1-2 Mb


Positional cloning

20 Mb

Positional Cloning

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 mapping

crosses but only a handful of those have been successfully cloned


Using ancestral haplotypes to localize qtls

20 Mb

Using ancestral haplotypes to localize QTLs

C3H (susc.)

B6 (res.)

Critical Region


Using ancestral haplotypes to localize qtls1

20 Mb

Using ancestral haplotypes to localize QTLs

C3H (susc.)

B6 (res.)

DBA (susc.)

Critical Region


Using ancestral haplotypes to localize qtls2

20 Mb

Using ancestral haplotypes to localize QTLs

C3H (susc.)

B6 (res.)

DBA (susc.)

Critical Region

One can then also use the map to:

- examine correlation of genotype to phenotype of other strains in the critical segments

- choosing optimal additional strains for crossing


Pilot haplotype map

Pilot Haplotype Map

  • ~150 SNPs across 25 Mb of chromosome 4

  • Typed in 37 inbred lines and 10 wild-derived isolates of potential founder strains

  • Roughly 3-fold less dense than projected to give a finished picture


Strains proposed

Strains proposed


First few mb

First few Mb…

Chr 4 35.7 37.6 37.9 39.4

(Mb)


Regional comparison 129 s1 vs c57bl 6j

Regional Comparison 129/S1 vs. C57BL/6J

{

{

Blue = ancestrally identical

Red = ancestrally divergent

A

G

T

T

T

A

A

T

C

T

A

G

T

A

C

C

C

A

C

A

G

A

A

C

A

C

C

T

A

*

T

G

C

C

A

A

G

G

T

A

*

C

C

C

*

C

G

G

T

A

C

G

A

G

G

G

C

A

G

A

A

C

A

C

C

T

A

G

T

G

C

C

A

A

G

G


Qtl identified in two crosses

QTL identified in two crosses

129xB6

DBAxB6


Qtl identified in three crosses

QTL identified in three crosses

  • QTL identified by three crosses 1x2, 1x3, and 1x4

  • Across 25 Mb, only 4 segments (each between 300 and 700 kb) are ancestrally consistent with the QTL mapping data

  • In total – 1.9 out of the 25 Mb is identified as most likely to contain the responsible mutation


A j vs c3h

A/J vs C3H

Not a software bug – two strains identical at every SNP typed

across the 25 Mb interval


Genetic background of the inbred lab mice1

Genetic Background of the inbred lab mice

C57BL/6

musc

domest

musc

C3H

domest

musc

domest

{

DBA

domest

cast

domest

musc

Avg segment size ~ 1-2 Mb


Genetic background of the inbred lab mice2

Genetic Background of the inbred lab mice

C57BL/6

musc

domest

musc

C3H

domest

musc

domest

{

DBA

domest

cast

domest

musc

Avg segment size ~ 1-2 Mb


Colleagues

Colleagues

Claire Wade

Andrew Kirby

Whitehead Genome Center

Kerstin Lindblad-Toh

EJ Kulbokas

Elinor Karlsson

Mike Zody

Eric Lander

Mouse Genome Sequencing Consortium


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