UCSC Genome Browser, Blat & Blast - Variants and Associated Genes With Disease Phenotypes - Report Assignment Help

Assignment Task    

Commence 

Regarding the 35 sources, you can use less or more, as needed. You noticed that it is not a direct writing assignment, it's more like a homework, each task should be done separately. You must reference the tools/websites you are using, just say that this tools/websites is used for this assignment. Basically, what this practical is asking you to do is use up all the different type of databases    and tools we have discussed in the lectures and extract information that we are discussing here.

These two sets actually come from an association study, the coming tasks will try to understand more about the disease biology or trade association behind it.

Please arrange all the answers in tables, and write paragraphs in between to link them or explain, the writing in between should be plus or minus 2000 word, that is why all the answers should be in tables because of the word limit.

Please look at the document attached

Practical Assignment

Prepare a word document, use tables to arrange the data of each task alone, also use figures, not exceeding 2000 words excluding Tables and references. and list URLs as references.

1. Introduction
2. Objectives of this practical

The purpose: This is in the context of signals coming from an Association study and you:

• try to understand the relationship of the different variants and associated genes with disease phenotypes you know.
• refer to a number of computational tools stroke databases that are available too.

3. Tasks ...1,2,3,4,5,6,7,8,9,10... (in the order provided)
4. Conclusions
5. Discussion

Task 1: Two lists (23 gene names) & (21 DNA sequence variants), the selected genes are part of a study. Establish the correct gene(s) – variant pairs using a genome browser; variants may also be located outside a gene; typically, the nearest gene(s) to this variant will be included in the list.

Take SNP ID, search it in one of the databases and check what are the traits that are associated
to this.

Task 2: Use database resources to explore what is known about the function of each gene and the protein it encodes (i.e. a few sentences summarising what the gene does) as well as its tissue expression profile, it is important to understand where the gene is expressed and its tissue expression profile.

Task 3: Establish the functional impact of each sequence variant; for example, is a variant located in a coding region of the genome and if yes, does it alter an amino acid? or is it overlapping a regulatory element? Report this element e.g. promoter

Task 4: Are there any good proxy SNPs (r2 ≥ 0.8) for the variants rs7636 and rs13107325?. Take two variants and it is asking you to establish whether there are other variants in linkage disequilibrium, so that's what we call Proxies. And if you remember, variants are in LD when they are (R2) square is above 0.8. IMPORTANT - in question 4, we do not want a simple yes/no answer, we are asking you to list the proxies

Task 5: Report, where possible, the minor allele frequency of each variant in the population reference the data source you used (e.g. URL of data base or repository). Use a database to report MAF in different population groups i.e. HapMap / 1000Genomes panels. Discuss if you observe any frequency differences between populations. Mostly use the 1000Genomes data to report minor allele frequencies in different populations. But Hapmap information is also fine. And discuss a little bit your observations in terms of frequency for this variant between populations.

Task 6: Investigate using both variant identifier (SNP) and the gene name whether there is a known association to one or more human traits (e.g. blood pressure) including disease. Use Genome Wide Association Study GWAS, or other type of genetic study where you have a robust finding.

Task 7: For those genes you have established an association to a human trait(s), report the number of known rare variants and how many of these rare variants are Loss of Function. So you need that data set to be able to address then the next one which is asking you for those genes you have established an association to human genome trait to actually. list the number of known rare variants and how many of these rare variants are loss of function.

Task 8: Does rs13107325 have any unusual features in terms of its LD relationship to other nearby common variants in European-descent populations? In which common diseases this variant may play a role?

Task 9: Based on all the information assembled, assess whether the genes found in question 7 could be divided in to subgroups underlying a specific trait or combination of traits. Start to grope the information that you have assembled so far, it is asking wither the genes found in question 7 could be divided into subgroups underlining a specific trait or combination of traits. Based on all the information assembled, assess whether the genes found in question 7 could be divided into subgroups underlying a specific trait or combination of traits.

Task 10: Are there any epigenetic effects known to be associated with the trait(s) of the subgroup(s) you defined (i.e. question 9 you need to address). Based on the subgroups that you have identified in nine, is there any literature out there talking about also epigenetic associations with the trades of the subgroups.

Remember until 9 you are looking at Genetic Association, so let's say you find group which has to do with blood pressure, and the question that is asking you in 10 is that if you look in the literature, are there known epigenetic effects associated with blood pressure? So when I assign the gene to a certain diseases, let's say that one gene is associated with bipolar, the other gene associated with depression and such, will the subgroups will be psychiatric disorders. Yeah, so that's what you have to decide.

So when I assign the gene to a certain diseases, let's say that one gene is associated with bipolar, the other gene associated with depression and such, will the subgroups will be psychiatric disorders. Yeah, so that's what you have to decide.

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