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Recently I went through a paper about hepatocellular carcinoma in which they talked about trunk genes (p. 26, second paragraph):

Branching tumor evolution complicates efforts to implement personalized medicine and suggests that targeted therapies might be directed to genes that are mutated at the trunk of the evolutionary tree. Transposons provide powerful tools for identifying trunk genes, as insertions in trunk genes are more likely to be associated with a higher number of sequencing reads.

I really don’t understand what are the trunk genes. Can anyone please explain them clearly.

Thank you

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  • $\begingroup$ I've tidied up you question a little and given focus to the key concept at issue — the "genes at the trunk of the evolutionary tree". $\endgroup$
    – David
    Commented Apr 24, 2017 at 16:17

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I think the article is using a phylogenetic tree to explain the stages of how the tumor has evolved.

According to Nature.com >>

All trees have a shared 'trunk', which represents the complement of mutations shared by all malignant cells within the cancer.

Or simplified by Britannica.com >>

Phylogenetic tree, also called Dendrogram, a diagram showing the evolutionary interrelations of a group of organisms derived from a common ancestral form. The ancestor is in the tree “trunk”; organisms that have arisen from it are placed at the ends of tree “branches.”

For a visual representation, this is a phylogenetic tree for evolution of breast cancer >>

Tree

Image Source: Phylogenetic Cancer Trees

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  • $\begingroup$ My first few readings of the sentence, I thought the article meant the ontogenetic tree -- that is, the mutation occurred early in the life of that specific individual. From the word "evolutionary", though, I think you are right. Still, the confusion is a warning to technical writers to use metaphors only very carefully. $\endgroup$
    – Michael Lorton
    Commented Apr 24, 2017 at 17:51
  • $\begingroup$ @Malvolio I had the similar confusion, although upon reading the abstract the OP has provided, I am pretty sure the trunk genes they have mentioned in the context of evolutionary trees is what I have answered. Needless to say, I totally agree with you about the careful use of these terms. $\endgroup$
    – Imtiaz Raqib
    Commented Apr 24, 2017 at 18:27
  • $\begingroup$ @user3351523 My pleasure. Glad I could help. $\endgroup$
    – Imtiaz Raqib
    Commented Apr 25, 2017 at 12:39

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