Genetic relationship lab questions

  1. [Coefficient of coancestry] Why do we see blocks of patterns in the heatmap? Is there something you can infer from the pedigree?
  2. [Coefficient of fraternity] Can you describe any difference between the heatmaps for coancestry versus fraternity?
  3. [Parentage inference] Can you roughly count the number of recombination events in one RIL?
  4. [Additive GRM] Why are the values in the diagonals larger than the values in the off-diagonals?
  5. [Dominance GRM] Do we need D-GRM in an inbred population, and why?
  6. [Compared A/D-GRM to coancestry/fraternity] Why is there such a large discrepancy between the estimates from pedigree- vs marker-based coefficients?
  7. [Additive x additive GRM] Can you explain why the AA versus A values have a quadratic/U-shaped distribution?
  8. [Splitting and combining GRM] Why is the LOCO-GRM not perfectly correlated to the original GRM?
  9. [Fst] Which (sub)-population is most genetically distant from the overall population, and why?
  10. [Genome-wide Fst] If 0.15 is out cutoff, do we have any significant marker differentiating the two (sub)-populations?
  11. [Roger’s/Nei’s distance] Can you describe any difference or similarity between these two trees?
  12. [PCA] Roughly how many principal components are needed to explain 50% of the variation seen here?
  13. [PCA] Can you describe what are each of the principal components separating?
  14. [Population admixture] Which K do you think is the right one for this dataset?
  15. [GWAS] Can you describe what is the difference in the GWAS results with and without population structure control?
Updated on February 5, 2024