Define "Germline" and "somatic" on genomic-variation/baselines-for-variation

[alanhoyle]

One thing that confused at first when I got into bioinformatics/cancer biology were the words "germline" and "somatic" as those mean different things in general biology and cancer biology.

I wasn't sure how to fit the stuff below on the baselines-for-variation page, otherwise I would have submitted something like this in a pull request.

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In the general context of biology, "germline" refers to a cell type, and means "cells that are involved in reproduction and can turn into the genetic information passed on to progeny" and "somatic" means "all the cells that are not involved in reproduction."

In cancer biology, "germline" refers to the genome and variants of the specific individual organism and means "the base genetic variants inherited from that organism's parents" and "somatic" means "Variants that occurred during the life of the organism in some cells but not others"

If you extract and sequence the DNA from almost any random sample of normal tissue, you can find that organism's germline variants. If you do the same from a tumor sample and screen out the background germline variants, you'll likely find the somatic variants that exist in that tumor.