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Genetics of Gene Expression <ul><ul><li>Chris Cotsapas </li></ul></ul><ul><ul><li>[email_address] </li></ul></ul>
Outline <ul><li>Background </li></ul><ul><ul><li>Significance </li></ul></ul><ul><ul><li>Experimental design </li></ul></u...
In the beginning... <ul><li>King and Wilson,  Science  1975 </li></ul><ul><li>Chimp – human coding sequence differences do...
Genetics of gene expression <ul><li>Find genetic variation that (partially) controls levels of RNA </li></ul><ul><li>If RN...
Experimental design <ul><li>Protein measurements </li></ul><ul><ul><li>2D gels; quantitation hard; resolution? </li></ul><...
Experimental design - methods <ul><li>Allelic discrimination </li></ul><ul><ul><li>SBE </li></ul></ul><ul><ul><li>Pyrosequ...
Experimental design - samples <ul><li>Pedigrees – multiplex/trios </li></ul><ul><ul><li>HapMap </li></ul></ul><ul><li>Popu...
Definitions Cis Trans
Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Populat...
First forays <ul><li>Damerval et al 1994 </li></ul><ul><li>Protein levels are different in 42/72 maize gene products </li>...
Cowles  et al  2002 <ul><li>F1 mice </li></ul><ul><li>69 genes in three tissues </li></ul><ul><li>4 variant; 2 only in liv...
Yeast WG approaches <ul><li>Brem  et al  Science 2002 </li></ul><ul><li>Linkage in 40 offspring of lab x wild strain cross...
Trans  hotspots Brem  et al  Science 2002
Yvert  et al  Nat Genet 2003
Mammals I <ul><li>F2 mice on atherogenic diet </li></ul><ul><li>Expression arrays; WG linkage </li></ul>Schadt  et al Natu...
Mammals II Chesler  et al  Nat Genet 2005 10% !!
Mammals III <ul><li>No major  trans  loci in humans </li></ul><ul><ul><li>Cheung  et al  Nature   2003 </li></ul></ul><ul>...
What's the deal with  trans ? <ul><li>Artefacts </li></ul><ul><ul><li>Normalization robustness </li></ul></ul><ul><ul><li>...
Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Populat...
<ul><li>trans -acting factors may be tissue specific </li></ul><ul><ul><li>TFs, signalling molecules, etc etc </li></ul></...
Examples <ul><li>Chesler vs Bystrykh (Nat Genet 2005)‏ </li></ul><ul><ul><li>39/101 (39%) forebrain  cis  in HSC </li></ul...
Correlation networks persist across tissues
Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Populat...
Slide courtesy Alkes Price
Population differences could have non-genetic basis  •  Differences due to environment?  (Idaghdour et al. 2008)‏ •  Diffe...
Gene expression experiment Does gene expression in 60 CEU + 60 YRI vary with ancestry? Does gene expression in 89 AA vary ...
Gene expression differences in African Americans validate CEU-YRI differences c  = 0.43 (± 0.02)‏ ( P -value < 10 -25 )‏ 1...
Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Populat...
Does GGE matter? <ul><li>Where is the phenotype? </li></ul><ul><ul><li>Case/control differences? </li></ul></ul><ul><li>Do...
Insight <ul><li>Mechanism? </li></ul><ul><li>trans  – coregulated groups? </li></ul><ul><ul><li>pathways </li></ul></ul><u...
IRGM  harbors a 20-kilobase deletion polymorphism immediately upstream IRGM Individuals Position on chr5 Slide courtesy St...
IRGM  structural haplotypes have altered expression Slide adapted, courtesy Steve McCarroll McCarroll  et al., Nature Gene...
IRGM expression levels influence the efficacy of autophagy McCarroll  et al., Nature Genetics , Sept. 2008 Slide adapted, ...
Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Populat...
Success? <ul><li>Baseline variation - tricky </li></ul><ul><li>Perturbations and phenotypes </li></ul><ul><ul><li>mouse ob...
Stuff we haven't covered <ul><li>Coregulated sets </li></ul><ul><li>Disease context  </li></ul><ul><li>Annotation/pathway ...
 
 
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Genetics of gene expression primer

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Broad Institute/MPG primer lecture given 2008-12-11. Thanks to Alkes Price and Steve McCarroll for contributing slides.

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Transcript of "Genetics of gene expression primer"

  1. 1. Genetics of Gene Expression <ul><ul><li>Chris Cotsapas </li></ul></ul><ul><ul><li>[email_address] </li></ul></ul>
  2. 2. Outline <ul><li>Background </li></ul><ul><ul><li>Significance </li></ul></ul><ul><ul><li>Experimental design </li></ul></ul><ul><ul><li>Definitions </li></ul></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight (?)‏ </li></ul><ul><li>Last thoughts </li></ul>
  3. 3. In the beginning... <ul><li>King and Wilson, Science 1975 </li></ul><ul><li>Chimp – human coding sequence differences don't match phenotypic distance </li></ul><ul><li>Gene regulation responsible for rest? </li></ul><ul><li>Basis for evo-devo, GGE </li></ul>
  4. 4. Genetics of gene expression <ul><li>Find genetic variation that (partially) controls levels of RNA </li></ul><ul><li>If RNA levels are different, maybe protein levels are also different </li></ul><ul><li>If protein concentration is different, maybe there is a phenotype? </li></ul>
  5. 5. Experimental design <ul><li>Protein measurements </li></ul><ul><ul><li>2D gels; quantitation hard; resolution? </li></ul></ul><ul><li>RNA measurements </li></ul><ul><ul><li>Expression chips ca. 1995 (Schena et al , Science)‏ </li></ul></ul>
  6. 6. Experimental design - methods <ul><li>Allelic discrimination </li></ul><ul><ul><li>SBE </li></ul></ul><ul><ul><li>Pyrosequencing </li></ul></ul><ul><ul><li>SNP arrays </li></ul></ul><ul><li>Whole-genome expression assays </li></ul><ul><li>Genotypes? </li></ul>
  7. 7. Experimental design - samples <ul><li>Pedigrees – multiplex/trios </li></ul><ul><ul><li>HapMap </li></ul></ul><ul><li>Population samples </li></ul><ul><li>Inbred strain panels </li></ul><ul><ul><li>genotypes </li></ul></ul><ul><li>New crosses </li></ul><ul><li>Inter-specific hybrids </li></ul>
  8. 8. Definitions Cis Trans
  9. 9. Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight (?)‏ </li></ul><ul><li>Last thoughts </li></ul>
  10. 10. First forays <ul><li>Damerval et al 1994 </li></ul><ul><li>Protein levels are different in 42/72 maize gene products </li></ul><ul><li>2D electrophoresis, eyeball spot quantitation </li></ul><ul><li>Problems: </li></ul><ul><ul><li>genome coverage </li></ul></ul><ul><ul><li>quantitation </li></ul></ul><ul><ul><li>post-translational modifications </li></ul></ul>
  11. 11. Cowles et al 2002 <ul><li>F1 mice </li></ul><ul><li>69 genes in three tissues </li></ul><ul><li>4 variant; 2 only in liver </li></ul>
  12. 12. Yeast WG approaches <ul><li>Brem et al Science 2002 </li></ul><ul><li>Linkage in 40 offspring of lab x wild strain cross </li></ul><ul><li>1528/6215 DE between parents </li></ul><ul><li>570 map in cross </li></ul><ul><ul><li>multiple QTLs </li></ul></ul><ul><ul><li>32% of 570 have cis linkage </li></ul></ul><ul><li>262 not DE in parents also map </li></ul>
  13. 13. Trans hotspots Brem et al Science 2002
  14. 14. Yvert et al Nat Genet 2003
  15. 15. Mammals I <ul><li>F2 mice on atherogenic diet </li></ul><ul><li>Expression arrays; WG linkage </li></ul>Schadt et al Nature 2003
  16. 16. Mammals II Chesler et al Nat Genet 2005 10% !!
  17. 17. Mammals III <ul><li>No major trans loci in humans </li></ul><ul><ul><li>Cheung et al Nature 2003 </li></ul></ul><ul><ul><li>Monks et al AJHG 2004 </li></ul></ul><ul><ul><li>Stranger et al PLoS Genet 2005, Science 2007 </li></ul></ul><ul><ul><li>Further scans (WT, Cheung, Schadt etc)‏ </li></ul></ul>
  18. 18. What's the deal with trans ? <ul><li>Artefacts </li></ul><ul><ul><li>Normalization robustness </li></ul></ul><ul><ul><li>Replication? </li></ul></ul><ul><ul><li>Clusters of correlated genes </li></ul></ul><ul><li>Power </li></ul><ul><ul><li>trans often weak effects </li></ul></ul><ul><ul><li>Small sample sizes </li></ul></ul>
  19. 19. Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight (?)‏ </li></ul><ul><li>Last thoughts </li></ul>
  20. 20. <ul><li>trans -acting factors may be tissue specific </li></ul><ul><ul><li>TFs, signalling molecules, etc etc </li></ul></ul><ul><li>cis regulatory sequences may be used by TS factors </li></ul><ul><li>So, shouldn't genetic effects on GE be tissue specific? </li></ul>Logic
  21. 21. Examples <ul><li>Chesler vs Bystrykh (Nat Genet 2005)‏ </li></ul><ul><ul><li>39/101 (39%) forebrain cis in HSC </li></ul></ul><ul><ul><li>297/1218 (24%) HSC cis in forebrain </li></ul></ul><ul><li>Hubner (Nat Genet 2005)‏ </li></ul><ul><ul><li>311/4297 (7%) shared between fat and kidney </li></ul></ul><ul><li>Campbell et al (Gen Res 2008)‏ </li></ul><ul><ul><li>12% of ~100 genes vary in at least one of three tissues </li></ul></ul>
  22. 22. Correlation networks persist across tissues
  23. 23. Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight (?)‏ </li></ul><ul><li>Last thoughts </li></ul>
  24. 24. Slide courtesy Alkes Price
  25. 25. Population differences could have non-genetic basis • Differences due to environment? (Idaghdour et al. 2008)‏ • Differences in cell line preparation? (Stranger et al. 2007)‏ • Differences due to batch effects? (Akey et al. 2007)‏ (Reviewed in Gilad et al. 2008)‏ Slide courtesy Alkes Price
  26. 26. Gene expression experiment Does gene expression in 60 CEU + 60 YRI vary with ancestry? Does gene expression in 89 AA vary with % Eur ancestry? 60 CEU + 60 YRI from HapMap, 89 AA from Coriell HD100AA Gene expression measurements at 4,197 genes obtained using Affymetrix Focus array c Slide courtesy Alkes Price
  27. 27. Gene expression differences in African Americans validate CEU-YRI differences c = 0.43 (± 0.02)‏ ( P -value < 10 -25 )‏ 12% ± 3% in cis Slide courtesy Alkes Price
  28. 28. Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight </li></ul><ul><li>Last thoughts </li></ul>
  29. 29. Does GGE matter? <ul><li>Where is the phenotype? </li></ul><ul><ul><li>Case/control differences? </li></ul></ul><ul><li>Does it translate to protein? </li></ul><ul><li>Can we reconstruct networks/pathways? </li></ul>
  30. 30. Insight <ul><li>Mechanism? </li></ul><ul><li>trans – coregulated groups? </li></ul><ul><ul><li>pathways </li></ul></ul><ul><li>Model QTs </li></ul><ul><li>Molecular variation snapshots </li></ul><ul><ul><li>What does it mean? </li></ul></ul><ul><li>Ancillary information </li></ul>
  31. 31. IRGM harbors a 20-kilobase deletion polymorphism immediately upstream IRGM Individuals Position on chr5 Slide courtesy Steve McCarroll McCarroll et al., Nature Genetics , Sept. 2008 rs13361189 (strongest Crohn’s-associated SNP)‏
  32. 32. IRGM structural haplotypes have altered expression Slide adapted, courtesy Steve McCarroll McCarroll et al., Nature Genetics , Sept. 2008
  33. 33. IRGM expression levels influence the efficacy of autophagy McCarroll et al., Nature Genetics , Sept. 2008 Slide adapted, courtesy Steve McCarroll
  34. 34. Outline <ul><li>Background </li></ul><ul><li>Basic findings </li></ul><ul><li>Tissue specificity </li></ul><ul><li>Population differences </li></ul><ul><li>Biological insight (?)‏ </li></ul><ul><li>Last thoughts </li></ul>
  35. 35. Success? <ul><li>Baseline variation - tricky </li></ul><ul><li>Perturbations and phenotypes </li></ul><ul><ul><li>mouse obesity crosses (Schadt et al )‏ </li></ul></ul><ul><ul><li>Drug screening (Choi, Yelensky et al )‏ </li></ul></ul><ul><ul><li>Crohn's disease (McCarroll et al )‏ </li></ul></ul>
  36. 36. Stuff we haven't covered <ul><li>Coregulated sets </li></ul><ul><li>Disease context </li></ul><ul><li>Annotation/pathway analysis </li></ul><ul><li>Modelling QTLs </li></ul><ul><li>Regression </li></ul><ul><li>WGAS </li></ul><ul><li>Multiple data sets/types </li></ul><ul><li>Post-transcriptional event variation </li></ul>
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