Question about Somatic and Germline with homozygous and heterozygous

Question

[mangfu100]

Hi.

I post a question continuously.

In this question , curious things are about somatic and germline.

Please see the below paragraph with bold text.

At every position where one or both samples had a variant, VarScan performs a direct comparison between tumor and normal genotype and supporting read counts to determine the somatic status. (I do understand so far but next sentence is confused to me)

Variants present in both samples are classified as somatic , variants heterozygous in the normal but homozygous in the tumor are classified as LOH(loss of heterozygosity) , and variant shared between samples are classified as germline.

the second sentence above, What is the difference between somatic and germline?

The sentence that Variants present in both samples are confused in meaning. I knew that somatic mutation is that the variants only exist in tumor sample, but reading and thinking again that sentence .., I can't connect the somatic concept I already knew.

and also I post a question before , but re-question about homozygous and heterozygous.

how can we define homo or hetero considering we have a only one pair of chromosome ?

I can't imagine the homo or hetero in next-seq, because I knew that the only one pair of chromosomes is sequenced...

Am I misunderstanding about concept?

I hope you understand my fuzzy questions.

I am looking forward to your answer

Thank you!

Answer 1

[Sebastian Boegel]

A somatic variant (=mutation) is a mutation that happens at some point in your life. This variant differs to what is hardcoded in your genome at birth. In cancer genomics, e.g. if you want to find somatic mutations, which means acquired mutations that are unique to the cancer cells (either as a cause or a consequence of the cells transforming into tumor cells), you usually compare the tumor genome against the wildtype (germline) genome of the same individual (e.g. PBMCs, healty tissue). If you variant in the tumor but not in the germline, this could be a hint for a somatic mutation.

Here is a simplified example explaining hetero and homozygosity:

Lets assume, we have a diploid cell (which is not always the case for e.g. tumor cells which can have copy number variations). If variant A (e.g. a SNV) is homozygous, you expect to see 100% of the reads from your exome-seq or wgs (lets assume NGS doesnt produce errors) containing this variant. If this variant is heterozygous (so one chromosome has the variant A and the other has the wildtype B), you expect to see 50% of the reads to contain A and 50% of the reads to contain B.

Note, that this explanation is for DNA-Seq, not for RNA-Seq.

Maybe this publication is also useful for understanding the very interesting field of allele frequencies:

http://www.nature.com/srep/2014/140422/srep04743/full/srep04743.html

[Jeff.B.Gaither]

I'm actually puzzled by this too (Sebastian, thanks for your response, but it doesn't totally answer my question.) In the above parapra, we get the conditions

"Variants present in both samples are classified as somatic" "variant shared between samples are classified as germline"

I think the OP was asking, what is the difference between these two conditions? To me they seem, if not equivalent, then at least extremely similar.