View source for QuBi/modules/biol203-geno-pheno-association-2020

; <div style="font-size:180%">BIOL 203 Bioinformatics Exercises for Lab 13</div>
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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):

<center>
Table 1. Sample Genotype Frequencies
{| class="wikitable"
|-
! !! T/T !! T/C !! C/C !! Total
|-
| Case || 0 || 24 || 127 || ?
|-
| Control || 9 || 68 || 114 || ?
|-
| Total || ? || ? || ? || ?
|}
</center>

Association between the genotype and the phenotype could be assessed with a [http://en.wikipedia.org/wiki/Contingency_table contingency table analysis]. In this case, &Chi;<sup>2</sup> = 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 [http://www.physics.csbsju.edu/stats/contingency.html 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 &Chi;<sup>2</sup> 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?
<center>
Table 2. Sample Allele Frequencies
{| class="wikitable"
|-
! !! T !! C !! Total
|-
| Case || ? || ? || ?
|-
| Control || ? || ? || ?
|-
| Total || ? || ? || ?
|}
</center>

===Test association with locus A===
Following the above two examples, perform both the genotype and allele association tests using the class data.
<center>
Table 3a. Genotype counts at Locus A
{| class="wikitable"
|-
!  !! A1/A1 !! A1/A2 !! A2/A2 !! Row Sum
|-
| Taster || ? || ? || ? || ?
|-
| Non-Taster || ? || ? || ? || ?
|-
| Column Sum || ? || ? || ? || ?
|}
</center>

Calculate allele counts & then test for association
<center>
Table 3b. Allele counts at Locus A
{| class="wikitable"
|-
!  !! A1 !! A2 !! Row Sum
|-
| Taster || ? || ? || ?
|-
| Non-Taster || ? || ? || ?
|-
| Column Sum || ? || ? || ?
|}
</center>
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
<center>
{| class="wikitable"
|-
!  !! B1/B1 !! B1/B2 !! B1/B3 !! B2/B2 !! B2/B3 !! B3/B3!! Row Sum
|-
| Taster || ? || ? || ? || ? || ? || ? || ?
|-
| Non-Taster || ? || ? || ? || ? || ? || ? || ?
|-
| Column Sum || ? || ? || ? || ? || ? || ? || ?
|}
</center>
Calculate allele counts & then test for association
Table 4b. Allele counts at Locus B
<center>
{| class="wikitable"
|-
!  !! B1 !! B2 !! B3 !! Row Sum
|-
| Taster || ? || ? || ? || ?
|-
| Non-Taster || ? || ? || ? || ?
|-
| Column Sum || ? || ? || ? || ?
|}
</center>
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 [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558&LINK_LOC=blasthome 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?