accelerating positional cloning in mice using ancestral haplotype patterns
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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Accelerating positional cloning in miceusing ancestral haplotype patterns
Mark Daly
WhiteheadInstitute for Biomedical Research
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Kerstin Lindblad-TohWhitehead/MIT Center for Genome Research
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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”
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Mouse history
Mouse Genetics, L. Silver
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Recent mouse history
W.E. Castle C.C. Little
Fancy mouse breeding - Asia, Europe(last few centuries)
Retired schoolteacher Abbie Lathropcollects and breeds these mice
Granby, MA – 1900
Castle, Little and others form most commonly usedinbred strains
from Lathrop stock(1908 on)
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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
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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
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Distribution of variation rates 70 unlinked 50 kb segments (129 vs. B6)
{
<1 SNP/10 kb
{~40 SNP/10 kb
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Distribution of variation rates 70 unlinked 50 kb segments
{
Only 1/3 validate
{~99% validate
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Low and High SNP rate suggest recent and distant
ancestry
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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
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Genetic Background of the inbred lab mice
musc musc
musc
musc
domest
domestdomest
domestdomest
C57BL/6
C3H
DBA
Avg segment size ~ 1-2 Mb{cast
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Positional Cloning
C3H (susceptible)
B6 (resistant)
20 Mb
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 handful of those have been successfully cloned
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Using ancestral haplotypes to localize QTLs
C3H (susc.)
B6 (res.)
Critical Region
20 Mb
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Using ancestral haplotypes to localize QTLs
C3H (susc.)
B6 (res.)
DBA (susc.)
Critical Region
20 Mb
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Using ancestral haplotypes to localize QTLs
C3H (susc.)
B6 (res.)
DBA (susc.)
Critical Region
20 Mb
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
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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
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Strains proposedWild derived ancestral strains Inbred strains
CAST/Ei M.m.castaneus
129S1/SvImJ C57BL/6J DDK NZW/LacJ
WSB/Ei M.m.domesticus
129X1/SvJ C57BLKS/J FVB/NJ PL/J
PERA/Ei M.m.domesticus
A/J C57BR/cdJ I/LnJ RIIIS/J
MOLF/Ei M.m.molossinus
AKR/J C57L/J KK/HlJ RF/J
MAI/PasM.m.musculus
BALB/cByJ C58/J LG/J SEA/GnJ
CZECHII/Ei M.m.musculus
BTBR+Ttf/tf CBA/J LP/J SJL/J
SPRET/Ei M.spretus
BUB/BnJ CE/J MA/MyJ SM/J
SEG/Pas M.spretus
C3H/HeJ DBA/2 NOD/LtJ ST/bJ
BACT/Bon
M.m.bactrianusC57BL/10 020 NON/LtJ SWR/J
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First few Mb…129S1 T A * C C C * C G G T A C G A G G G
AKR A G T T T A A T G G T A C G A G G G
A_J A G T T T A A T G G T A C G A G G G
BALB_c T A * C C C G C G G T A C G A G G G
C3H A G T T T A A T G G T A C G A G G G
C57B6 A G T T T A A T C T A G T A C C C A
CBA A G T T T A A T C T A G T A C C C A
DBA2 A G T T T A A T C T A G T A C C C A
FVB A G T T T A A T C T A G T A C C C A
I A G T T T A A T G G T A C G A G G G
NOD A G T T T A A T G G T A C G A G G G
NZB * A C C C C * C C T * G T A C C C A
SJL A G T T T A A T C T A G T A C C C A
SWR A G T T T A A T C T A G T A C C C A
Chr 4 35.7 37.6 37.9 39.4 (Mb)
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Regional Comparison 129/S1 vs. C57BL/6J
Red = ancestrally divergent
{
GGGAGCATGGC*CCC*AT
ACCCATGATCTAATTTGA
{
GGAACCGTGATCCACAAGAC
GGAACCGT*ATCCACAAGAC
Blue = ancestrally identical
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QTL identified in two crosses
129xB6
DBAxB6
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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
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A/J vs C3H
Not a software bug – two strains identical at every SNP typedacross the 25 Mb interval
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Genetic Background of the inbred lab mice
musc musc
musc
musc
domest
domestdomest
domestdomest
C57BL/6
C3H
DBA
Avg segment size ~ 1-2 Mb{cast
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Genetic Background of the inbred lab mice
musc musc
musc
musc
domest
domestdomest
domestdomest
C57BL/6
C3H
DBA
Avg segment size ~ 1-2 Mb{cast
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Colleagues
Claire WadeAndrew Kirby
Whitehead Genome CenterKerstin Lindblad-TohEJ KulbokasElinor KarlssonMike ZodyEric Lander
Mouse Genome Sequencing Consortium