Entering edit mode
8.6 years ago
ceruleanivy
▴
50
I have two problems when it comes to detecting LOH events in my tumor samples: a) My mutation calling software provides LOH evidence only when the normal sample is heterozygous (regardless of VAF) and there are zero reads on the variant for the tumor sample. However, there are many cases (not to say most) where the tumor cell content is not 100% and therefore it is likely that a LOH event might give lower, although not zero, VAF in the tumor sample compared to the normal. How am I supposed to detect all LOH events ? a) There are regions within the same gene where some variants have the requirements to be characterized as somatic mutations while others follow the LOH conditions. What should I report ?
