Assignment

Suppose you are a conducting a research project to determine genetic variants that cause a fraction of people to be highly resistant to alcohol intoxication. You decide to do a GWAS by enlisting several thousand college students around the country to take part. Your research team performs tests on each subject to measure how cognitive and physical performance is affected following a certain amount of alcohol consumption (adjusted for body weight, of course). You then perform SNP genotyping all the students, and identify a haplotype that is strongly associated with alcohol resistance. This haplotype spans 25 kb and contains 2 genes (Gene A and Gene B).

Sequencing reveals that there are 4 variants (SNPs and indels) in this region that are unique to the resistant students. You believe that one of these variants, listed below, is "causative" for resistance:

Variant #1: A SNP that changes a highly conserved amino acid in Gene A.

Variant #2: A SNP in the 5' UTR of Gene B. (UTRs can have a role in mRNA transcript stability and translation.)
Variant #3: A 3 bp insertion in the region between the two genes.
Variant #4: A single nucleotide change near an intron/exon junction of Gene B.

Your task: Design experiments to identify which of the variants causes the phenotype, and the molecular mechanisms by which a responsible variant may cause the phenotype. Propose experiments to evaluate the phenotypic impact of each of the variants, and make hypotheses to explain how each variant may be acting. You should suggest a combination of bioinformatic analyses of available data, plus new experiments. You should discuss how certain types of existing data might influence the experiments you design.