A paper studying a lung cancer genome the way it should be done, using fresh samples from a live patient with known smoking record has appeared in Nature on 27.5., page 473. Of course, as the papers using cell lines got the scoop, this one wasn't hyped or reported in the press, so I managed to miss it and only discovered it when going back to the issue to look up something else. Goes to show that cutting corners pays off nicely in science. Still, lots more studies like this one are needed before one can arrive at definitive conclusions.
The current issue of Nature includes a news piece relating criticism of "cancer genome" sequences based on cell lines, which I have also voiced here. After some ifs and buts, the piece fails to come to a clear conclusion.
Personally, I wouldn't mind people sequencing the old cell lines if they think it helps them understand all the research that has been done on them in the past decades. What annoys me is the claim that this is "the cancer genome" and tells us something important about how cancer works. If the papers appeared in some middling journal for the record, that would be fine. But as articles in Nature, they are automatically overhyped in the press.
I think to find out something meaningful about real cancers, one would need to advance a bit more carefully and study proper cancer cells (the argument that in real tumours cancer cells are mixed with healthy cells doesn't stand up, as 1) it is now possible to sequence DNA on single molecule basis, thus from single cells, and 2) if they want lots of cancer cells, they just have to sort them out).
And of course, after all that huffing and puffing, the journal goes ahead and publishes another big "article" by the same people, also based on cell lines. I still think this is just cutting corners to be quicker than the people who do the research properly, and to get all the rewards that come with a "first" being published in Nature or Science. (And I am speaking as someone who has also been a co-author of an "article" in Nature in my time, and I'd also be happy to tell you what was wrong with that paper!)