QuBi/modules/biol203-geno-pheno-association-2020

BIOL 203 Bioinformatics Exercises for Lab 13

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Test phenotype-genotype association

Introduction: GWAS & Contingency Test

Genome-Wide Association Study (GWAS) is a method for mapping phenotypes to genotypes. In a typical GWAS study, frequencies of alleles (e.g., C or T at position 785) are determined in a sample of affected individuals (the "cases" e.g. disease) as well as in a sample of unaffected individuals (the "controls"). For example, the following table shows results of a hypothetical case-control study at a locus segregating with two alleles (C and T):

Table 1. Sample Genotype Frequencies

	T/T	T/C	C/C	Total
Case	0	24	127	?
Control	9	68	114	?
Total	?	?	?	?

Association between the genotype and the phenotype could be assessed with a contingency table analysis. In this case, Χ² = 26.4, p<0.0005, suggesting a significant association between genotypes and diseases. (By comparing the expected and observed counts, one could conclude that the C/C genotypes are over-represented in disease cases.)

1. Perform an online contingency table analysis using the hypothetical data in Table 1. Click on "other contingency tables" and do a 2-rows and 3-columns test with the data above. Your Χ² should be 26.4.

2. Deriving from Table 1, fill the following table with allele counts. Then perform a 2-by-2 contingency table analysis using the link above. For example, in the controls, the number of T alleles is: 18 + 68 = 86 , because homozygotes have two alleles and heterozygotes have one.

Is there a statistically significant association between alleles and disease phenotype? Which allele (C or T) is over-represented in (i.e., statistically associated with) disease cases?

Table 2. Sample Allele Frequencies

	T	C	Total
Case	?	?	?
Control	?	?	?
Total	?	?	?

Test association with locus A

Following the above two examples, perform both the genotype and allele association tests using the class data.

Table 3a. Genotype counts at Locus A

	A1/A1	A1/A2	A2/A2	Row Sum
Taster	?	?	?	?
Non-Taster	?	?	?	?
Column Sum	?	?	?	?

Calculate allele counts & then test for association

Table 3b. Allele counts at Locus A

	A1	A2	Row Sum
Taster	?	?	?
Non-Taster	?	?	?
Column Sum	?	?	?

1. 1. Record your result in the lab report sheet for the contingency test for Locus A, including chi-square statistic, degree of freedom, and p values

Test association with Locus B

Table 4a. Genotype counts at Locus B for each phenotype

	B1/B1	B1/B2	B1/B3	B2/B2	B2/B3	B3/B3	Row Sum
Taster	?	?	?	?	?	?	?
Non-Taster	?	?	?	?	?	?	?
Column Sum	?	?	?	?	?	?	?

Calculate allele counts & then test for association Table 4b. Allele counts at Locus B

	B1	B2	B3	Row Sum
Taster	?	?	?	?
Non-Taster	?	?	?	?
Column Sum	?	?	?	?

1. 1. Record your result in the lab report sheet for the contingency test for Locus A, including chi-square statistic, degree of freedom, and p values

Web Exercise. Search for gene information using NCBI online databases

1. Point your browser to the NCBI Human Genome Resource page
2. Copy and paste sequence provided on Blackboard- this is the sequence of the gene associated with the taster phenotype
3. Press "BLAST". Copy & Paste the top hit in your final lab report.
4. Briefly describe the function of the gene based on information found on the locus page

Additional questions

Answer briefly (1-2 sentences):

1. 1. State what is the null hypothesis in a chi-square test & what is the alternative hypothesis
   2. Explain what probability is represented by the p-value.
   3. What can you conclude when p-value is below the threshold of significance (e.g., p = 0.05)?
   4. What would you conclude when p-value is above the critical value?
   5. Is there a statistically significant association between one of the alleles tested and the Taster phenotype?
   6. Which genotype is over-represented in the Non-Tasters?
   7. Which allele is over-represented in the Non-Tasters?