HRD score LST?
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?
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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.
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