Although the validity of many such patents has recently been in doubt, a landmark ruling by the US Federal Court of Appeals last week (Association for Molecular Pathology v. USPTO; the Myriad gene patent litigation) reaffirmed their validity. E.g. http://www.phgfoundation.org/news/9422
Is anyone clear on what this ruling really means? Is a gene patented for a specific purpose e.g. prognosis or diagnosis of a specific condition - or does it become off-limits for further research, unrelated to the original use/purpose?
To me that sounds like common sense, in the same way one cannot patent "gold", "platinum", or "elephants", even if they are hard to catch or find.
Justice Thomas wrote: “A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated…It is undisputed that Myriad did not create or alter any of the genetic information encoded in the BRCA1 and BRCA2 genes”.
Just read the full ruling hoping for some clarification on the validity of a cDNA patent; there's a note that since intron sequences are removed cDNA is not natural and thus patentable (except for small cDNA that are derived from genomic segments that do not contain introns). I wonder what implications the cDNA ruling has for RNA-seq protocols.
I do not think the court has considered the case of RNA-seq at all, where cDNA is generated via random primers or polyA priming of all -naturally occurring, with removed exons from naturally occurring splicing events- transcripts in an undirected fashion. I don't want to give anyone ideas, but in an extreme case, all RNA-sequencing involving reverse transcription and cDNA, could be an infringement. I think that this is excessive. But, as a precaution, I would (at least in the US where the patent applies) automatically mask the BRCA regions from any alignment, thus yielding 0 coverage, or do the sequencing where the patent isn't aplicable, e.g. Europe or China.
Then, there will be no evidence that any cDNA ever was created for this region, and there will be no way to prove infringement, such that the lab can plausibly deny existence of cDNA of patented regions after cDNA has been discarded.
One view to take is when it comes to bioinformatics and recent changes in the world of gene patents, the ruling has little bearing on the day to day activities of the bioinformatics group. What the ruling does mean is the bioinformatics group/scientist needs to engage the intellectual property group of lawyers and their assistants in order that both sides agree to a strategy to take up work on certain genes or gene sequences.
In other words, the bioinformatics researchers should not act (i.e., engage in decision-making) without having this conversation. Universities, institutes, gov't labs and for-profits all have lawyers to deal with invention disclosures. Make a phone call and start the conversation.
Sensible advice, but how does this effect genome-wide studies that implicitly work on all genes regardless of patent position? Should results from such studies be manually screened with a view to patent infringement? Should this be done automatically by the bioinformatics software itself? Had anyone recreated e.g. the WTCCC experiments against a human genome sequence that has been masked for all patented sequences? Has anyone even constructed such a sequence?
I'd still go to my colleagues in legal and ask. I do know that for most patents on genes, there is no to little restriction on their use in a purely academic, not-for-profit setting.
I don't know if anyone really knows at this point. In case you haven't seen it, there's another detailed post on Genomics Law Report about this latest ruling:
Contributory infringement, [...], usually consists of selling a component of a
patented invention, knowing that the component has no use except in that invention.
So components that have uses other than in that invention might be safe from indirect infringement. This probably makes unintentional infringement of isolated gene patents by generic bioinformatics tools somewhat unlikely.
why should developers be concerned? Surely it's the user that should be concerned isn't it?
Is anyone clear on what this ruling really means? Is a gene patented for a specific purpose e.g. prognosis or diagnosis of a specific condition - or does it become off-limits for further research, unrelated to the original use/purpose?