Lecture 10 Quiz

What is the primary aim of a genome-wide association study (GWAS)?

• To map all genes in the human genome

• To identify associations between environmental exposures and disease

• To identify associations between genetic variants and traits/diseases

• To determine protein-protein interactions

What does a Manhattan plot show?

• Gene expression levels across tissues

• P-values of SNP-trait associations across the genome

• Pairwise sequence similarity

• Results of multiple sequence analysis

What is linkage disequilibrium (LD)?

• Random association of SNPs in the genome

• Association of alleles that are inherited together due to physical proximity

• Recombination between distant loci

• Variants that occur only in coding regions

Which of the following best describes population stratification?

• A technique for genotyping individuals

• Statistical noise in the GWAS output

• Differences in allele frequencies due to ancestry rather than true association

• Errors in DNA sequencing

What does the Bonferroni correction do?

• Increases sensitivity to rare variants

• Adjusts P-values to account for the number of tests performed

• Randomizes the dataset

• Controls for linkage disequilibrium

Can a SNP located in a non-coding region of the genome affect disease susceptibility?

• No - if it is non-coding, it won't do anything at the protein level

• Yes - non-coding mutations at the promoter region may disrupt transcription factor binding and gene expression

• Yes - mutations in non-coding regions could still cause changes to amino acid sequences

• No, non-coding regions are not transcribed nor translated, so they are irrelevant

Suggest one bioinformatics approach that could be used to explore the regulatory function of this SNP.

• Phylogenetic tree construction

• Genome assembly

• Transcription factor binding site analysis

• Restriction site recognition