Cluster and clone are the same?

[Tato14]

Thanks for the great tool.

I am checking some results and looking at the plots, I see that you used two different terms in the vignette: cluster and clone. The "cluster" term is used in the "3. Clusterning [...]" section and "clones" in the "4. Tree inference" section.

I am completely new to the field but seems to me that this terms have different meaning but I am unsure how to interpret them. Could you please confirm that you used this words with different meaning? And could you explain it a little bit to pinpoint the difference?

Thanks

[RachelKarchin]

Thanks for the question! The "mutation clusters" consist of mutations with similar cancer cell prevalence across one or multiple samples, so these mutations are inferred to be in the same cells. The "clone" or "subclone" is an aggregation of mutation clusters as you traverse the evolutionary tree.

1 o
/
2 o 4 o
|
3 o

In this tree (which is rendering strangely here), the node "1" is the clonal mutations.
Node "2" represents a mutation cluster, and also a subclone which is comprised of all mutations in node 1 and node 2
Node "3" is a mutation cluster and also a subclone comprised of all mutations in nodes 1, 2, and 3

It may be easier to visualize the mutation clusters (except for node 1) on the edge of the tree upstream of a node, and to have the nodes themselves represent the subclones.

Hope this helps!