I read the X-23 comics a little while back, and after recently finishing a novel I find it hard to believe that X-23 wasn't either completely based on this novel or almost completely based off of it. The novel is Dean Koontz's Sole Survivor. (THE REST OF THE POST WILL HAVE SPOILERS FOR THE BOOK)
In the novel, it turns out a woman and a young child have survived an unsurvivable plane crash. Late in the book, it is discovered that the woman works for Project 99, a top-secret agency tasked with taking samples of blood from children deemed to have "supernatural" abilities, such as telepathy or telekinesis in order to find the specific genetic markers causing the abilities. Beyond this, the agency has used these genes and has created a handful of children out of scratch, one of which is a young girl named CCY 21-21, sound familiar?
The resemblances are astonishing. The idea to create CCY 21-21 was that of the woman who worked at Project 99, named Rose. In X-23, it is the idea of Sarah Kinney to clone Wolverine's genes to make X-23. After leaving the facility in Sole Survivor, both Rose and CCY 21-21 become targets, and Rose ends up dead when all is said and done. In X-23, the Kinney and X-23 are targets when they leave the facility and Kinney ends up dead after everything is said and done. Also, in Sole Survivor, CCY 21-21 views Rose as her mother and calls her mom. In X-23, X-23 views Kinney as the same, although the comic goes one step further in actually making Kinney X-23's biological mother.
After reading the novel, I just felt that the similarities were to significant to be of simple coincidence. I find it hard to believe that Craig Kyle and Christopher Yost simply came up with the idea for the Innocence Lost storyline without taking part of it from Sole Survivor. If they did, they did a real good job in coming up with a story so extremely similar to Sole Survivor.