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

imported>Lab at 21:37, 7 May 2020

2020-05-07T21:37:59Z

← Older revision		Revision as of 21:37, 7 May 2020
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	# Press "BLAST". Copy & Paste the top hit in your final lab report.		# 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		# 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===		===Additional questions===

imported>Lab at 01:04, 7 May 2020

2020-05-07T01:04:00Z

← Older revision		Revision as of 01:04, 7 May 2020
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	\|}		\|}
	</center>		</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		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===		===Test association with Locus B===
	Table 4a. Genotype counts at Locus B for each phenotype		Table 4a. Genotype counts at Locus B for each phenotype
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	\|}		\|}
	</center>		</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		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==		==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		# 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

imported>Lab at 01:03, 7 May 2020

2020-05-07T01:03:02Z

imported>Lab at 01:01, 7 May 2020

2020-05-07T01:01:44Z

← Older revision		Revision as of 01:01, 7 May 2020
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	# Briefly describe the function of the gene based on information found on the locus page		# Briefly describe the function of the gene based on information found on the locus page

	==Additional questions==		===Additional questions===
	#Answer briefly (1-2 sentences):
			Answer briefly (1-2 sentences):
	## State what is the ''null hypothesis'' in a chi-square test & what is the ''alternative hypothesis''		## 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.		## Explain what probability is represented by the p-value.

imported>Lab: /* Additional questions */

2020-05-07T01:00:05Z

Additional questions

← Older revision		Revision as of 01:00, 7 May 2020
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	==Additional questions==		==Additional questions==
	Answer briefly (1-2 sentences):		#Answer briefly (1-2 sentences):
	## State what is the ''null hypothesis'' in a chi-square test & what is the ''alternative hypothesis''		## 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.		## Explain what probability is represented by the p-value.

imported>Lab at 00:59, 7 May 2020

2020-05-07T00:59:08Z

← Older revision		Revision as of 00:59, 7 May 2020
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	\|}		\|}
	</center>		</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===		===Test association with Locus B===
	Table 4a. Genotype counts at Locus B for each phenotype		Table 4a. Genotype counts at Locus B for each phenotype
Line 100:		Line 100:
	\|}		\|}
	</center>		</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==		==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		# 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
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	# Briefly describe the function of the gene based on information found on the locus page		# Briefly describe the function of the gene based on information found on the locus page

	==~~Lab Report IV~~==		==Additional questions==
	~~# Your report should include the following results:~~		Answer briefly (1-2 sentences):
	~~## 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 the sequence provided~~
	~~Additional questions to include in your report~~:
	## State what is the ''null hypothesis'' in a chi-square test & what is the ''alternative hypothesis''		## 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.		## Explain what probability is represented by the p-value.
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	## Which genotype is over-represented in the Non-Tasters?		## Which genotype is over-represented in the Non-Tasters?
	## Which allele 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~~

imported>Lab at 16:14, 6 May 2020

2020-05-06T16:14:15Z

← Older revision		Revision as of 16:14, 6 May 2020
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	</center>		</center>
	Calculate allele counts & then test for association		Calculate allele counts & then test for association
	Table 4b. Allele counts at Locus A		Table 4b. Allele counts at Locus B
	<center>		<center>
	{\| class="wikitable"		{\| class="wikitable"
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	# 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		# 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		# Copy and paste sequence provided on Blackboard- this is the sequence of the gene associated with the taster phenotype
	~~# 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.		# Press "BLAST". Copy & Paste the top hit in your final lab report.
	# Briefly describe the function of the gene based on information ~~gathered~~ on the locus page		# Briefly describe the function of the gene based on information found on the locus page

	==Lab Report IV==		==Lab Report IV==

imported>Lab: 2020 page

2020-05-06T16:05:27Z

2020 page

New page

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

===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 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 provided on Blackboard- this is the sequence of the gene associated with the taster phenotype
# 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.
# Briefly describe the function of the gene based on information gathered on the locus page

==Lab Report IV==
# 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 the sequence provided
Additional questions to include in your report:
## 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?
## Are there exceptions? What are possible causes for exceptions?
## Define e-value in a BLAST search

← Older revision		Revision as of 01:03, 7 May 2020
Line 71:		Line 71:
	\|}		\|}
	</center>		</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		# 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===		===Test association with Locus B===
	Table 4a. Genotype counts at Locus B for each phenotype		Table 4a. Genotype counts at Locus B for each phenotype
Line 100:		Line 100:
	\|}		\|}
	</center>		</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		# 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==		==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		# 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
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	Answer briefly (1-2 sentences):		Answer briefly (1-2 sentences):
	## State what is the ''null hypothesis'' in a chi-square test & what is the ''alternative hypothesis''		# 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.		# 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 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?		# 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?		# 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 genotype is over-represented in the Non-Tasters?
	## Which allele is over-represented in the Non-Tasters?		# Which allele is over-represented in the Non-Tasters?