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. - PowerPoint PPT PresentationTRANSCRIPT
Accelerating positional cloning in miceusing ancestral haplotype patterns
Mark Daly
WhiteheadInstitute for Biomedical Research
Kerstin Lindblad-TohWhitehead/MIT Center for Genome Research
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 Genetics, L. Silver
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)
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
• 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)
{
<1 SNP/10 kb
{~40 SNP/10 kb
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
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
musc musc
musc
musc
domest
domestdomest
domestdomest
C57BL/6
C3H
DBA
Avg segment size ~ 1-2 Mb{cast
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
Using ancestral haplotypes to localize QTLs
C3H (susc.)
B6 (res.)
Critical Region
20 Mb
Using ancestral haplotypes to localize QTLs
C3H (susc.)
B6 (res.)
DBA (susc.)
Critical Region
20 Mb
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
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 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
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)
Regional Comparison 129/S1 vs. C57BL/6J
Red = ancestrally divergent
{
GGGAGCATGGC*CCC*AT
ACCCATGATCTAATTTGA
{
GGAACCGTGATCCACAAGAC
GGAACCGT*ATCCACAAGAC
Blue = ancestrally identical
QTL identified in two crosses
129xB6
DBAxB6
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
Not a software bug – two strains identical at every SNP typedacross the 25 Mb interval
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
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
Colleagues
Claire WadeAndrew Kirby
Whitehead Genome CenterKerstin Lindblad-TohEJ KulbokasElinor KarlssonMike ZodyEric Lander
Mouse Genome Sequencing Consortium