On graph-based representations of a (set of) genomes

In 1986, in a letter to the journal Nature, James Bruce Walsh and Jon Marks lamented that the upcoming human genome sequencing project “violates one of the most fundamental principles of modern biology: that species consist of variable populations of organisms”. They further wrote: “As molecular biologists generally ignore any variability within a population, the individual whose haploid [sic] genome will be chosen will provide the genetic benchmark against which deviants are determined”. They conclude that ” ‘the’ genome of ‘the’ human will be sequenced gel by acrylamide gel”.

We have come a long way when it comes to taking population variation into account in molecular/genetic/genomic studies. But these sentiments, expressed already in 1986, echo some of the trends in the human genetics field: the move away from a single, linear representation of ‘the’ human genome. In this post I will provide some background, explain the reasons for moving towards graph-based representations, and indicate some challenges associated with this development.

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