7.11 Homework
7.11.0.1 Learning Objectives
- Interpret the summary statistics typically reported in GWAS studies
- Understand the limitations and biases of GWAS
7.11.0.2 Assignment
Find any GWAS paper. Read it and report:
- Phenotype being studied
- Sample size
- Population being studied (homogeneous? Multi-ethnic? If it’s multi-ethnic, how do they correct for the effect of ancestry?)
- For the top asssociation:
- p-value (would you call it significant genome wide?)
- Effect size
- Did the authors replicate the result in an independent cohort?
- Haplotype structure, nearby genes, causal variant
Example solution
Example GWAS: Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.
- Phenotype: Number of children ever born
- Sample size:: 785,604
- Population: European; no population structure correction (but did control for family structure)
- Top asssociation: rs201815280,
chr3:85546181,A->ACACC(from Supp. Table 7)- p-value:
5.25e-26, seems genome-wide significant - Effect size:
0.0249(with every copy of theACACCallele, individuals have one more child born) - Replication: Did not replicate in a cohort of 34,367 women from the FinnGen study (p =
0.177) - Haplotype structure, nearby genes, causal variant: In an intron of CADM2; no causal variant or LD analysis
- p-value: