The key case to watch is in re Bilski which was argued before the Supreme Court last November but has not yet been decided. This relates to business method patents, but the Court of Appeals decision was very broad and restricted such patents to those making a "transformation" or involving a "machine." It was a very poor decision in my opinion, produced by judges that don't understand computers for one thing. (The notion that something could be an invention if you hardwire it, but not if you write a program to perform the exact same activity on a general-purpose computer is naive beyond words).
The court here followed Bilski in overruling the MYGN process patents here. Hopefully this decision will serve as a wake-up call to the Supreme Court about how much of an overreach the appeals court decision in Bilski was.
Anyhow, if the Supreme Court overrules or narrows Bilski, then tests for biomarkers and the like should again become patentable. I personally see no rationale for allowing a composition of matter patent for a gene though.
(BTW, Bilski was a really broad and stupid patent for hedging commodities that should never have been granted in the first place for other reasons).
Peter