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hartwigmedical / hmftools

Various algorithms for analysing genomics data
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How can we identify LOH on some HLA allele in Lilac's output? #327

Closed Biojenifer closed 2 years ago

Biojenifer commented 2 years ago

Hi!

I was wondering how can we identify LOH in some HLA allele in Lilac's output. Should we look at TumorCopyNumber column?

For example:

I get a TumorCopyNumber of 0.64 for B*51:01 allele in one of my samples. Does this mean LOH for this allele?

Thanks!

p-priestley commented 2 years ago

LILAC leverages PURPLE copy number fitting and assigns to the alleles based on the relative support for each allele.

We normally use a rule of alleleCopyNumber (ie TumorCopyNumber column) < 0.5 as LOH. Generally fitted copy number is close to integer, but 0.64 is unclear and could indicate noise, a poor fit or subclonal loss of the allele so in this case it may not be super clear.