QuBi/modules/biol203-geno-pheno-association

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BIOL 203 Summer 2020 - Bioinformatics Exercises for Lab 11

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 ? ? ?

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 A

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

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. Expand the "Algorithm parameters" tab and change "Expect threshold" to 0.00001 (10e-5). Define "expect value" in your owns words after watching the linked Youtube video.
  4. Press "BLAST". Copy & Paste the top hit in your final lab report.
  5. Briefly describe the function of the gene based on information gathered on the locus page

Lab Report IV

  1. Your report should include the following results:
    1. A printout of contingency test for Locus A, including expected counts, observed counts, chi-square statistic, degree of freedom, and p values
    2. Same as above for Locus B
    3. A printout of alignment for the top BLAST hits for the sequence provided

Additional questions to include in your report:

    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?
    8. Are there exceptions? What are possible causes for exceptions?
    9. Define e-value in a BLAST search
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