I have read paper VarScan2 : somatic mutation and CNA discovery today.
In the paper, I didn't understand the statement below.
VarScan performs a direct comparison between tumor and normal genotypes and supporting read counts to determine the somatic status. Variants present in both samples are classified as somatic, variants heterozygous in the normal but homozygous in the tumor are classified as LOH, and variants shared between samples are classified as germline.
The bold texts is that I can't understand the concept.
Firstly, I don't know the difference between germline and somatic considering the context above. I have already knew that germline is that varaints that also exist in tumor and normal but somatic is that variants only exist in tumor. but above sentence is so confused. I think the author wrote the sentence not clear. Is that right?
Secondly, I don't understand variants classified as LOH. Is it really important to classify variants considering homozygous and heterozygous? I don't know the reason why VarScan2 classify according to homozygous variants in tumor sample. What is the real meaning of homozygous in the tumor but heterozygous in normal samples? Is that important to consider? I don't know..
my background is computer science not biology, so homozygous and heterozygous concept are always very hard to understand.
I hope you understand.