I think it was in the 2002 official manga, that everything was finally nailed down and established with regards to her childhood. Some of it was laid out in the Nintendo Power comic from 1994, specifically Chapter 4:
And then later expanded upon in the newer games, like the Prime series, and I think the Zero Mission remake might mention some of her past in the intro scroll, been a while since I played it so I don't recall.
We are of course also dealing with a game that has had its story mangled left and right by localizations. In the US release of Metroid for the NES, Samus Aran was a man, and a cyborg:
Though to be fair, I've seen it later claimed that this was intentional "to keep her true gender a secret until the end of the game". So who knows.