What are Manhattan Plots – How are they useful for displaying SNPs?
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A Manhattan plot in genome wide associations studies(GWAS) is a graph that displays which individual allele has a likelihood of being involved in whatever trait you are doing the graph to study.
To see that we need a bit of math and the concept for the graph itself. Sorry it’s a bit technical but I’ll explain terms as I go.
Each point on the graph represents a variant of a gene, called an allele. Think of genes as the box to hold a trait, and the allele as what you put into the box. So you have a gene for eye color, but the allele will be for blue, green, brown, etc. Genes in a species are usually always in the same place on our chromosomes. For humans and the eye example, each person has two paired chromosomes, each chromosome has an eye color gene, in the same place. So we’d have two alleles for each eye color gene. And these studies take in usually thousands of people, so double the amount for alleles.
Along the X axis, you have the location of each gene. Since each allele for a specific gene is in the same spot, if you were to draw a vertical line at any particular gene location, your line would run through every allele, for that gene, your subjects as a whole have. So if you have 100 people and you’re looking at Gene X, you would have 200 data points on that vertical line.
On the Y axis is how likely that allele is to be involved in the trait you are looking for. To keep with the eye color example, say we’re looking for blue eyes. On that vertical line at the eye color gene, you’ll end up with two separated groups of dots, the ones at the bottom will be for all the other eye colors, the ones at the top will be the ones for blue eyes. But if you look at all the other genes along the X-axis, you’ll see mostly random points with the vast majority of them at the bottom of the graph since they aren’t involved in eye color.
The reason they’re so great for SNPs is that SNPs are usually either one thing or another, they don’t usually have spectrum effects. If you have allele A the switch for whatever trait is on, if you have allele B/C/D-Z that switch is off.
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