Show threadGraham CoopMay 16, 2023
These plots were inspired by plots in Brian Donovan et al [https://onlinelibrary.wiley.com/doi/10.1002/sce.21506 ] and Biddanda, Rice, Novembre https://elifesciences.org/articles/60107 and uses the latter’s geovar package. #VisualizingHumanGeneticDiversity 8/n
Show threadGraham CoopMay 16, 2023
We can also place this Euler diagram in the broader context of the whole genome.
#VisualizingHumanGeneticDiversity
7/n
Show threadGraham CoopMay 16, 2023

The ACB (red) and ASW (blue) share nearly all the variation found in the other samples, and due to their high levels of genetic diversity, some of that variation is not common in the other samples from the Americas.

This does not mean that these variants are completely absent from the other groups, but instead, that these variants are rare or undetected in the other samples included in the figure.

#VisualizingHumanGeneticDiversity

6/n

Show threadGraham CoopMay 16, 2023
We visualized the overlap of common variation using an Euler diagram in the 1000 genomes Americas samples (colours same as tweet 4). There is clear overlap of common variation between the samples. #VisualizingHumanGeneticDiversity 5/n
Show threadGraham CoopMay 16, 2023
Samples from the Americas differ in their number of common variants. For example, there’s more common variation in the African Caribbean in Barbados (ACB) and African Ancestry in Southwest US (ASW) samples #VisualizingHumanGeneticDiversity 4/n
Show threadGraham CoopMay 16, 2023
We looked at genetic differences between samples from the Americas (1000 Genomes Project). Variants are found at a small fraction of sites in these genomes and most variants are at low frequencies. Only a few reach the level to be classified as “common” (>5% frequency). #VisualizingHumanGeneticDiversity 3/n
Show threadGraham CoopMay 16, 2023
Humans are remarkably genetically similar to each other. Two human genomes selected at random differ only at roughly 1/1000 single nucleotide sites (e.g. your chromosome might have a T and another person’s an A). Most of this variation likely has no effect on traits. #VisualizingHumanGeneticDiversity 2/n
Graham CoopMay 16, 2023

A blog post by @kitchensjn
and me on visualizations of the sharing of human genetic variation 1/n

#VisualizingHumanGeneticDiversity

https://james-kitchens.com/blog/visualizing-human-genetic-diversity

Visualizing Human Genetic Diversity

A key insight from human genetics is that, as a species, we are all very genetically similar to one another and share much of our genetic variation. Our genome can be depicted as a string of letters (A, T, G, and C), referring to the four nucleobases found in DNA.

James Kitchens