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

; <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") 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.)

# Perform an [http://www.physics.csbsju.edu/stats/contingency.html online contingency table analysis] using the hypothetical data in Table 1.

# Deriving from Table 1, fill the following table with allele counts. Then perform a 2-by-2 contingency table analysis using the link above. 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 at 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>

===Test association at 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 A
<center>
{| class="wikitable"
|-
!  !! B1 !! B2 !! B3 !! Row Sum
|-
| Taster || ? || ? || ? || ?
|-
| Non-Taster || ? || ? || ? || ?
|-
| Column Sum || ? || ? || ? || ?
|}
</center>

==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 at Locus A into the first text box (add a FASTA heading, e.g., ">Locus_A")
# 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.
# Press "BLAST". Copy & Paste the top hit in your final lab report.
# Repeat the above for the sequence at Locus B. Copy and paste the top hit in your final lab report.

==Lab Report & Exit Questions==
# Your report should include the following results:
## A printout of contingency test for Locus A, including expected counts, observed counts, chi-square statistic, degree of freedom, and p values
## Same as above for Locus B
## A printout of alignment for the top BLAST hits for Locus A sequence
## Same as above for Locus B
# Exit questions
## 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?
## Which of the two genes shows significant ''genotype'' association with the PTC Taster/Non-Taster phenotype?
## Is there a statistically significant association between the ''alleles'' and the Taster phenotype? 
## Which genotype is over-represented in the Non-Tasters?
## Which allele is over-represented in the Non-Tasters?
## Are there exceptions? What are possible causes for exceptions?
## Define e-value in a BLAST search