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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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Subclonal allele specific Copy numbers #37

Open compgenome365 opened 7 years ago

compgenome365 commented 7 years ago

Hi Venkat, I am trying to clarify about FACET's output when we have at least one subclone along with the clonal cluster. I understand that is indicated by K in FACET's notation with K=1 is clonal.

Now let's say we have K=3. Does FACET give the allele-specific copy numbers for all three subclones? From the output fit2$cncf, it seems only one major and minor CN is available for all the segments.

Am I missing something?

Thanks in advance --Subhajit

veseshan commented 7 years ago

For a specific locus if some cells have (m1,p1) parental copies and others (m2,p2) it leads to an identifiability issue that cannot be resolved for many (most) combinations since we don't see individual cells only the pool of DNA. Thus the subclonality in is only estimated at segment level where the copy number is the average of all the cells. We say segment 1 has (m1,p1) copies at cellular fraction cf1 and segment 2 has (m2,p2) copies at cellular fraction cf2.

Venkat