HRD score LST?

Question

[vctrm67]

I am confused about the calculation of LST score for the HRD score. Looking at the description of such a package that does this calculation (scarHRD):

In the LST figure B, I don't understand why the 2nd "X" in chromosome 1 is marked as an "X". It is between 2 adjacent breakpoints of >10 Mb, and the size is <3 Mb, no? Doesn't that fit the description? Also what is wrong with the 2 "X" marks on chromosome 2?

[jared.andrews07]

I agree, I'm not sure what the problem is with those either. You may consider opening an issue in the repo, though it looks like the dev isn't responding to any of those that are open. I guess you could also consider e-mailing the dev since they put their email address on the repo as well.

Answer 1

[e.rempel]

In the original paper by Popova, T the definition of LST is given as

the number of LSTs in the tumor genome was estimated for each chromosome arm independently (not accounting for the centromeric breaks)

Thats is why there is a grey rectangle in the mentioned figure, I think. It denotes a centromeric break.