As you correctly realized, the Indominus Rex never actually existed, they completely invented that creature, like the "asset" it was supposed to be. However, they didn't create it out of nothing either. Rather what they did was mix the DNA of various different dinosaurs and other animals they already had (which we can assume to be scientifically possible in the movie), like the Velociraptor, the T-Rex, and some existing animals like cuttlefish (gaining camouflage), tree frogs (gaining heat stealth) and others.

Claire: Our advances in gene splicing have opened up a whole new frontier...The Indominus Rex. Our first genetically modified hybrid.
Investor: How did you get two different kinds of dinosaurs to, you know...
Dr. Wu: Indominus wasn't bred. She was designed.

Afterall this is not a new concept in the universe of Jurassic Park. If you remember, in the first movie they completed the missing dinosaur DNA with that of frogs, which ultimately lead to them developing possibilities for reproduction on their own, even though they were all created as females.

And this is in fact also part of Dr. Wu's moral justification for creating that new "dinosaur". They made up all those dinosaurs in a lab from extinct DNA possibly mixed with some other DNA. So just mixing more animals and more dinosaurs into one was merely the next step in this process. You could say the Indominus Rex is as much of a real dinosaur and has as much natural right to exist as all the other "dextincted" dinosaurs (decide for yourself, though, how much right that is).

Dr. Wu: You are acting like we all engaged in some kind of mad science. But we are doing what we have done from the beginning. Nothing in Jurassic World is natural. We have always filled gaps in the genome with the DNA of other animals. And, if their genetic code was pure, many of them would look quite different.