This keeps on getting repeated so as a biology grad student I feel the obligation to inform everyone: yes, epigenetics is very important and makes up much of the story, but while a lot about it is still unknown, we have just as many tools to tackle it as we do with genomic DNA. We can sequence the epigenome (both histone marks and DNA CpG methylation), the transcriptome, the translatome, and the proteome (by mass spec, though not de novo) - almost any "ome" that involves any combination of nucleic acids and proteins can be probably sequenced and profiled by technology that we have today. The only thing that we probably can't easily do yet is metabolomics, because small molecules are not built out of well-understood monomeric units, but I bet there are tens if not hundreds of labs around the world working on this kind of technology as we speak.
My point is, the explosion in sequencing technology that have occurred in the 10 years since the completion of the human genome have put us solidly in the "post-genomics" era. The technologies to find the needle in the haystack exist in the here and now - the only real constraints are time, manpower (brainpower?), sample availability, and (to some extent) cost, in the sense that you need to not be in the bottom 30% of labs in terms of your funding situation in order to have enough money to be able to use these technologies. Brooke is human so there will be limitations in terms of what kinds of samples we can take without harming her health, but the people working on this will be able learn a lot from her genome (and her epigenome, transcriptome, and so on and so forth) and then they will be able to find those mutant candidate genes and make mouse or Drosophila models so that we can get a really detailed understanding of what is going on at the mechanistic level, and in those model organisms we can then whatever we want in order to get whatever types of data we need.
A reference for those who haven't seen it yet: http://www.genome.gov/sequencingcosts/