$r = \frac{\text{number of recombinant offspring}}{\text{total number of offspring}}$

Question 1

Which of the following best describes the main purpose of a Genome-Wide Association Study (GWAS)?

Accepted Answer

To locate causative genetic variation for a trait by detecting association between the trait and inheritance of SNPs at known genomic locations.

Question 2

Linkage disequilibrium (LD) is most likely to be observed between:

Accepted Answer

Alleles that are physically close together on the same chromosome.

Question 3

Why is linkage mapping most effective for Mendelian (monogenic) traits?

Accepted Answer

Because these traits are caused by alleles of a single gene, making statistical linkage easier to detect.

Question 4

Which equation best represents the recombination frequency ($r$) between two loci?

Accepted Answer

$r = \frac{	ext{number of recombinant offspring}}{	ext{total number of offspring}}$

Question 5

A Manhattan plot is used in GWAS to:

Accepted Answer

Show the statistical significance of association between SNPs and a trait across the genome.

Question 6

Which of the following is a limitation of linkage mapping in humans?

Accepted Answer

Pedigree information can be incomplete or incorrect, and related individuals may share many alleles.

Question 7

GWAS is particularly useful for identifying genetic variants associated with:

Accepted Answer

Complex traits caused by common alleles with small effects.

Question 8

Which statement about SNPs used in GWAS is correct?

Accepted Answer

SNPs are markers that may be in linkage disequilibrium with causative variants.

Question 9

In a GWAS, what is the first step after defining the study population?

Accepted Answer

Determine the genotype at mapping SNPs distributed throughout the genome for each individual.

Question 10

The 'common disease common variant' hypothesis underlying GWAS suggests that:

Accepted Answer

Common diseases result from alleles of multiple genes, each present at high frequency and with a small effect on phenotype.

Question 11

Which scenario best illustrates linkage disequilibrium?

Accepted Answer

Two alleles at different loci are inherited together more often than expected by chance due to their physical proximity on a chromosome.

Question 12

Why can it be difficult to detect statistically significant linkages for complex (multigenic) traits using linkage mapping?

Accepted Answer

Because the effect of each individual allele is small and may be masked by other genetic and environmental factors.

Question 13

After a region of the genome is identified by GWAS as associated with a trait, what is the next step?

Accepted Answer

Test the region for causative variation and determine the role of that variation in the trait.

Question 14

Which of the following best explains why closely linked SNPs remain in linkage disequilibrium over generations?

Accepted Answer

Because recombination between closely linked loci is rare.

Question 15

A researcher performs a GWAS and finds a SNP significantly associated with increased risk of a disease. What does this result most likely indicate?

Accepted Answer

The SNP is in linkage disequilibrium with a causative variant for the disease.

Question 16

Which of the following is NOT a step in conducting a GWAS?

Accepted Answer

Sequencing only the causative gene in all individuals.

Question 17

Which real-world example demonstrates the use of GWAS in medical genetics?

Accepted Answer

Identifying genetic variants associated with severe Covid-19 and respiratory failure.

Question 18

Which of the following best describes the relationship between recombination and linkage disequilibrium?

Accepted Answer

High recombination rates between loci decrease linkage disequilibrium.

Question 19

Which formula would you use to calculate the probability of two alleles being inherited together if they are in linkage disequilibrium?

Accepted Answer

$P_{AB} > P_A 	imes P_B$

Question 20

Which resource would you use to find published GWAS results for a specific disease?

Accepted Answer

The GWAS Catalog.

Genome-Wide Association Studies (GWAS) and Linkage Mapping in Genetics

Study Guide - Practice Questions