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Genome variation and function 2

Goal: Today, we learn about how to analyze genetic variants and its association with phenotype.

  1. Genome wide association study - theory

  2. Genome wide association study - browse real data

Relevant review papers if you want to further learn:

General

Depends on your interest:

Plant

Animal

Fish

1. Lecture part

PDF

Prologue - Current topics in genomics

Human genome sequence

Nobel prize 2022

We will learn about:

Methods and significance of functional genomics

Challenges of genomics

2. Hands-on tasks

Now, we will investigate real GWAS data at GWAS ATLAS, which concains 4,756 human GWAS across 3,302 traits.

Let’s explore the human GWAS database GWAS ATLAS. In the tutorial, I did not explain everything, so please explore it yourself and get familiarised with it.

Case study 1

Go to “Browse GWAS” in the top, black bar. And search for the trait about hair morphology and see the results.

Questions 1

Q1-1. Examine the Manhattan plot. Where do you see the peak? How can we interpret this?

Q1-2. See the left table. How many individuals were investigated?

Q1-3. How many variants were investigated?

Q1-4. See the table under the Manhattan plot with gene annotations. What is the ID of top-associated SNP? (SNP ID: rsXXXXX)

Q2-5. Go to GGV map browser and enter the SNP ID above to see the global distribution of this variant. “A” is the straight hair allele, and “G” is the curly hair allele. What can we estimate from this map? Why did it happen?

Result 1

Click to display

https://atlas.ctglab.nl/traitDB/4023

A1-1. There is one big peak at chromosome 2. It is plausible that one genetic factor with very strong effect is associated with this trait.

A1-2. 4878 individuals

A1-3. 560921 SNPs

A1-4. rs260643

A1-5. Straight hair type is thought to be adaptive in East Asia in human evolution. Why? There are a lot of theory but there is not a concrete consensus yet.

if you are interested In this paper, they generated a knock-in mouse model to investigate the function of hair-morphology altering variant. In the mouce model, they observed increased hair thickness, but also change the morphology of mammary and eccrine glands.

Case study 2

Go to “Browse GWAS” in the top, black bar. And search for the trait about eyesight and see the results.

Questions 2

Q2-1. Examine the Manhattan plot. Where do you see the peak? How can we interpret this?

Q2-2. See the left table. How many individuals were investigated?

Q2-3. How many variants were investigated?

Q2-4. See the bottom Manhattan plot with gene annotations. What is the top-associated gene?

Q2-5. (Discussion topic) - Do some literature search about the top-associated genes and assume how this gene is associated with the trait, “Reason for glasses/contact lenses: For short-sightedness”. To further understand the mechanism, what experiment would you plan?

Result 2

Click to display

https://atlas.ctglab.nl/traitDB/3539

A2-1. There are multiple peaks, in the chromosomes 1, 2, 4, 6, 8, 10, 15… The obserbation implies that multiple loci are associated with this trait (The trait is polygenic).

A2-2. 78647 samples (See the left box, “N”)

A2-3. 9223534 SNPs (See the left box, “Nsnps”)

A2-4. PRSS56 (the dot with lowest P-value = highest -log10P value)

A2-5. Put what you have discussed on CANVAS “Discussion” with the full names of participants who contributed to the discussion.