Tom Bishop
It Wandered In From the Wastes

Yeah if they needed untainted DNA then why didn't they keep everyone alive? Why did they choose Shaun of all people and what would've happened if you died and Shaun was unsuitable as a subject? Why didn't they head to a different vault in order to find viable subjects and why Vault 111 of all vaults was "so special"?
So many questions and from what some of you are saying, plotholes as well.
Ah, now this one does have a valid answer. It's the anthropic principle. There's nothing particularly special about Shaun or Vault 111. They could have gone to another vault. They could have taken another child. But they had to settle on someone, and to fuel the plot of the game, the protagonist is the parent of the abducted child. So, if Shaun didn't work out for whatever reason, and they ended up abducting an infant named, say, Joe, the protagonist would then be Joe's parent. And I actually kind of liked that there was such a plain and unremarkable reason to target Shaun and his parents. There were a lot of annoying messiah/chosen one undertones to the story in F3 that Bethesda really ought to have kept to TES, and so it was a pleasant surprise to hear that what started you out on your adventure this time around was nothing more than really shitty luck.