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Accelerating positional cloning in mice using ancestral haplotype patterns

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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  1. Accelerating positional cloning in miceusing ancestral haplotype patterns Mark Daly Whitehead Institute for Biomedical Research

  2. Kerstin Lindblad-Toh Whitehead/MIT Center for Genome Research

  3. 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”

  4. Mouse history Mouse Genetics, L. Silver

  5. 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

  6. 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

  7. 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

  8. Distribution of variation rates 70 unlinked 50 kb segments (129 vs. B6) { { <1 SNP/10 kb ~40 SNP/10 kb

  9. Distribution of variation rates 70 unlinked 50 kb segments { { Only 1/3 validate ~99% validate

  10. Low and High SNP rate suggest recent and distant ancestry

  11. 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

  12. 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

  13. 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

  14. 20 Mb Using ancestral haplotypes to localize QTLs C3H (susc.) B6 (res.) Critical Region

  15. 20 Mb Using ancestral haplotypes to localize QTLs C3H (susc.) B6 (res.) DBA (susc.) Critical Region

  16. 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

  17. 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

  18. Strains proposed

  19. First few Mb… Chr 4 35.7 37.6 37.9 39.4 (Mb)

  20. 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

  21. QTL identified in two crosses 129xB6 DBAxB6

  22. 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

  23. A/J vs C3H Not a software bug – two strains identical at every SNP typed across the 25 Mb interval

  24. 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

  25. 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

  26. 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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