QuBi/modules/biol203-geno-pheno-association-2020
- BIOL 203 Bioinformatics Exercises for Lab 13
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 | ? | ? | ? |
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 | ? | ? | ? | ? |
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
- Point your browser to the NCBI Human Genome Resource page
- Copy and paste sequence provided on Blackboard- this is the sequence of the gene associated with the taster phenotype
- Press "BLAST". Copy & Paste the top hit in your final lab report.
- Briefly describe the function of the gene based on information found on the locus page
- to get to the gene locus page: click on the link for your hit--click on the "Feature" link (link describes the gene product)--the next page will be a GenBank page with protein and DNA sequence-- find the "Gene ID" which is a four-digit number-- click on it and you will be directed to the locus page
Additional questions
Answer briefly (1-2 sentences):
- State what is the null hypothesis in a chi-square test & what is the alternative hypothesis
- Explain what probability is represented by the p-value.
- What can you conclude when p-value is below the threshold of significance (e.g., p = 0.05)?
- What would you conclude when p-value is above the critical value?
- Is there a statistically significant association between one of the alleles tested and the Taster phenotype?
- Which genotype is over-represented in the Non-Tasters?
- Which allele is over-represented in the Non-Tasters?