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« Court Report | Main | "Progress" on Senate "Patent Reform" Bill »

March 30, 2009

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Kevin, as usual, good analysis. I'm struck by the difference in approach here versus, say, last December's CAFC decision in Sanofi v Apotex. There, the CAFC said that a prior art publication that disclosed a racemate of a small molecule didn't anticipate the enantiomeric salt (b/c that enantiomeric salt wasn't actually shown) or render it obvious (for reasons largely tied to the particular facts of that case). Here, the court acknowledged that the claimed anti-sense oligos weren't disclosed; that fact alone should have been sufficient to avoid a lack of novelty rejection. There may or may not be a good argument in this case for obviousness, but the discrepancy in the treatment of anticipation regarding small molecules as opposed to nucleic acids is hard to swallow.

Kevin,

Is this case yet further evidence, like what transpired at oral argument in Kubin, that the Federal Circuit glosses over too much that these nucleotide materials have nuances that other chemical compounds don't have? Also, and along the vein of what Dan F. said, if the Federal Circuit's analysis is like you suggest ("[the Wraight reference] merely disclosed all 15-mer sense oligonucleotides, coupled with generic disclosure that antisense oligonucleotides would specifically hybridize to the disclosed sense oligonucleotides, and the knowledge in the art that such oligonucleotides could be made without undue experimentation"), shouldn't they be looking at this as an "obviousness" question under 35 USC 103, rather than "anticipation" under 35 USC 102?

Kevin,

Before I forget, I also agree with this statement of yours: "Gleave's arguments might have had additional force had they contained a functional limitation regarding operability as antisense oligonucleotides."

From Robert Cook-Deegan (who is having technology issues):

=======
(1) How does full genomic sequence information interact with the Court's logic? Most of the possible oligomers that would become composition of matter claims are in the public domain or patent prior art. Sequences processed from genomic DNA might still be unpredictable and thus new and nonobvious and there is a distinction, of course, of specific claimed sequences and binding domains with (partially) known function. But it seems like a fuzzy line. How will CAFC apply it?

(2) Is there any way to know how many sequence-based claims might be affected (e.g., likely to be found invalid if challenged) by this decision and Kubin?

Dear Dan:

The lynchpin of the analysis is that once you disclose sequence X, you disclose inherently its complement, sequence X'. And since the technology for making oligonucleotides is robust, any reference disclosing sense oligonucleotide Y also enables antisense oligonucleotide Y'. Because the court held there was no "and use" requirement for enablement of an anticipating reference (and Gleave's claims did not have a functional limitation anyway), the reference anticipated the claims.

Thanks for the comment.

Dear EG:

Well, I think if the panel was more concerned with accuracy they would have said that the antisense oligonucleotides were inherently disclosed and that was the anticipation. Treating this as an express anticipation case worked better for the court on many levels: as a question of fact, they could give Zurko/Gartside deference to the Office's factual determinations. They also could frame it as a black-and-white issue, making it easier to arrive at their conclusion. Finally, they knew that Gleave could get a method-of-use claim, so they were not foreclosing all patentable subject matter.

Thanks for the comment.


Nothing surprising about this holding. What's surprising is that is was appealed to the CAFC in the first place and they actually bothered to address the arguments.

"What was not anticipated by the cited art are methods of using these oligonucleotides, and the Court suggested that Gleave might be entitled to such claims."

And the earth continues to turn on its axis, just as before.

Dear Bob:

I think the point is that the oligomers were not in the prior art, at least not expressly. The cited art disclosed 15-mer sense oligonucleotides, and there was no indication that any overlapping antisense olionucleotides were in the art - at least no such art was cited.

I think a genuinely "new" genomic DNA sequence might well be patentable, but I suspect that this would be more likely to be the case if there was a gene/open reading frame that was separated by a lot of intervening sequence DNA. The human K-ras gene is an example: the size of the genomic DNA encompassing the gene is about 35 kilobases, for a gene encoded by a much smaller mRNA (around 1kb, as I recall). Under those circumstances, arguments could be made that the skilled worker would not have recognized the fragmented genomic ORF or that it was not properly annotated. cDNA library information would be another story, insofar as it existed.

I think the point is that the CAFC wants it to be a bright line - if the sequence was in the prior art, even if there was no know utility for it, then a claim to the nucleic acid per se is unpatentable. This does not stem from any incentive for disclosure; it comes from that branch of the patent law interested in preventing private parties from expropriating material already in the public domain.

I think the only way to "know" the fate of any particular sequence is to scour the publicly-available databases for any sequence of interest and determine whether the sequence was publicly available prior to the applicant's filing date. I suspect there will be some, but there is no way to know how many.

Let's wait for the CAFC's decision on Kubin before we discuss those possibilities.

Thanks for (being persistent about) the comment.

Dear Panic:

I am glad you are not surprised. We are not panicked, nor do we think the earth's axis is in jeopardy.

Could you provide any rationale for your view that this was the expected result? Especially in view of the lack of any express disclosure of an antisense oligonucleotide in the cited art, and the court's own admission that there was ample caselaw (albeit incorrect, in their view) supporting the proposition that an anticipating reference needed to disclose how to "make and use" the invention?

Inquiring minds would benefit from elucidation.

Kevin: "Gleave's arguments might have had additional force had they contained a functional limitation regarding operability as antisense oligonucleotides"

Um ... no.

Believe it or not, Kevin, sometimes people file applications describing compositions that simply aren't patentable no matter how much attorney money and time is wasted.

Kevin,

You stated: "Gleave's arguments might have had additional force had they contained a functional limitation regarding operability as antisense oligonucleotides". The decision plainly states this as well ("the simple fact is that Gleave's composition cliams do not require antisense activity....")

However, it seems like the court and Kevin's statements (and Gleave's counsel, apparently) don't give sufficient weight to the claim language "of sufficient length TO ACT AS AN ANTISENSE INHIBITOR OF human IGFBP-2 and human IGFBP-5." My reading of this is that the claims DO require antisense activity, just maybe not as precisely as they could have.

I agree, however, that this most likely wouldn't have affected the result. The court would have just had to address inherency. However, it bothers me that this apparently functional language was treated so dismissively.

Dear Frank:

Um . . . why?

Which is the point. Whether these particular applicants deserved a patent is certainly important to them, but my question is about the lines the CAFC draws, and the consequences (intended or otherwise). I think an argument could be made that this result would not have been attained if the molecules were traditional "small molecule" compounds, and I think the reason is the predictability of the sense/antisense complementarity. I don't know if I disagree with the result - I think the reasoning could have been clearer - but I do think we need to address the rationale if we are going to make sense of what is and is not patentable.

Thanks for the comment.

Dear CNS:

I could have been more clear. I think this language was insufficient because it was related so strongly to the length limitation. The language says that the oligonucleotide is long enough to act as an antisense inhibitor, but it doesn't say that the antisense oligonucleotide was (i.e., was required to be) an inhibitor. I know this looks like a quibble, but there should be a reason for the court's dismissiveness of the limitation, and this is the best one I can think of.

Thanks for the comment.

Kevin: "Could you provide any rationale for your view that this was the expected result?"

Yes, that's quite easy. First, you wrote in your post that "Wraight ... disclosed all 15-mer sense oligonucleotides, coupled with generic disclosure that antisense oligonucleotides would specifically hybridize to the disclosed sense oligonucleotides"

So there you are. All the antisense sequences were disclosed. The only way it could get more express than that is if they were set forth one by one. Anticipatory dislcosure requirements are strict, but they ain't that strict.

"the court's own admission that there was ample caselaw (albeit incorrect, in their view) supporting the proposition that an anticipating reference needed to disclose how to "make and use" the invention"

Huh? Are you saying the court made new law here? I missed that part. I understand that there is plenty of mis-cited dicta on the books. But there is nothing unexpected about the CAFC ignoring that in favor of the well-understood law that has been applied for a long time: if one of skill in the art could make and use a composition, then the disclosure of that composition anticipates a claim to that composition. The disclosed sequences could be used as probes, if nothing else. That's more than enough to anticipate the composition.

Anyway, there you are. I expected the result based on those facts. If you didn't expect the result ... well, maybe it's why you also think that adding functional "limitations" to a composition claim (without changing the structure) changes the composition from one that is anticipated to one that isn't.

I know you're smarter than this, Kevin. Sometimes you just get carried away.

"However, it bothers me that this apparently functional language was treated so dismissively"

????

It's functional language tacked onto a composition claim that was anticipated by prior disclosure of THE COMPOSITION. Why should this "bother" anyone?

You know what would really be bothersome: if the CAFC allowed people to claim old compositions in composition claim format by reciting newly discoverded "functions." THAT would be bothersome.

Geez, people, save your angst for when the court really muffs it up. This decision is the right one.

Dear Frank:

You are correct that adding a functional limitation cannot make an old composition new. But there is some sense in the argument that the art did not disclose any antisense oligonucleotides at all. The court chose to say that the disclosure of sense oligonucleotides + complementarity + routine methods of making oligonucleotides was enough for the Wraight reference to provide an enabling and anticipating disclosure.

But let's say that some of the oligos worked and some of them didn't (which was an argument that Gleave used in prosecution and on appeal to the BPAI). In your view, would there be a composition of matter invention in determining which ones were functional antisense oligos, and then claiming this limited subgenus? If not, how does that square with chemical practice, where species encompassed by a generic claim are not anticipated by earlier generic disclosure, provided that the particular species is not expressly recited in the prior art? I think the court got around that by the complementarity relationship between sense and antisense oligonucleotides- although the court didn't say it directly - and that was the point of the post.

Thanks for the comment.

Frank, I didn't say the *result* bothered me. I don't think the result would have (or should have) been any different with a more clearly stated functional limitation. You admit yourself that it is "functional" language, and that's my point. The court seems to think that it is NOT functional, and I (and you) think it is.

My complaint is about the linguistic hair-splitting that the court appears to have done to avoid going into an inherency analysis. (It also certainly didn't help that Gleave's counsel conceded the point.)

Dear Panic:

Thanks for the complement, but it isn't as clear to me as it is to you.

The funny thing is that the prior art reference did list all 1400 15-mer sense oligos, so the idea that this may be required (Gleave speculated that it was motivated by written description concerns) isn't that far fetched. And actually the court went out of its way to clarify (in its view) the law of what was required for a reference to be sufficiently enabled to anticipate these claims. The court spent a good deal of its opinion refuting the idea - which Gleave supported by case law citations - that the art must enable the skilled worker to make AND use the claimed invention. From this case, it is very clear that the prior art must just enable the worker to make the claimed invention. Maybe not new law, but certainly a clarification. (Not to play "gotcha," but even you used the old "make and use" language in your comment, and that's what the court specifically did say (and it isn't dicta) - all the art has to do is enable the skilled worker to make the claimed invention.)

And with regard to "new law", it may be "new" in the sense that this is the first case (to my knowledge) where the existence of a sense-oriented oligonucleotide was found to anticipate an undisclosed antisense oligonucleotide. That may be the right decision - the post did not take the position that it was the wrong one - but I think we should discuss why it's the right decision.

As for the functional limitation question, see my response to Frank - again, I think the court applied the law differentially in this case as compared with chemical patent practice, and for the reasons discussed in that response. Whether it is a good idea (it certainly wasn't a clearly-asserted idea) is what blog posts are for.

Thanks for the comment.

Kevin "The court spent a good deal of its opinion refuting the idea - which Gleave supported by case law citations - that the art must enable the skilled worker to make AND use the claimed invention. From this case, it is very clear that the prior art must just enable the worker to make the claimed invention. "

I think that is overstating the holding in this case. The sense and antisense molecules that were disclosed in this case (and I'm not wasting any time with that "constroversy") have a utility. And its not even some post hoc utility set forth in a different reference (although that would certainly suffice for anticipation purposes here). It's set forth in the same reference that discloses the oligos: they could be used for specific hybridization to complementary sequences.

As the court notes, such a utility is unlikely to support a patent absent additional data. But it's perfectly fine for anticipation purposes.

Gleave seems to want to treat this reference as if it were a bunch of letters scrawled on the side of a bridge somewhere. Or some "fantastic" molecule whose only utility is as a food additive. That's simply not the case.

"In your view, would there be a composition of matter invention in determining which ones were functional antisense oligos, and then claiming this limited subgenus?"

You mean a novel composition consisting of oligonuclotides A, B, C, D and E? I have not read Wraight, but I believe such a claim would not be anticipated. A claim to a "An isolated oligo, wherein said oligo is generically defined as blah blah" is dead on arrival, of course, as every member of the genus is anticipated by Wraight (and it would only take one).

"If not, how does that square with chemical practice, where species encompassed by a generic claim are not anticipated by earlier generic disclosure, provided that the particular species is not expressly recited in the prior art?"

You have my answer. A better question is how does it NOT square?

Dear Panic:

Gleave argued that the prior art needed to establish a utility in order to anticipate, and the court said it did not:

"We have at times framed the issue of enablement under § 102 as a question of whether one of ordinary skill in the art would know how to “make and use” the invention based on the reference’s disclosure. See, e.g., Impax Labs., Inc. v. Aventis Pharms., Inc., 468 F.3d 1366, 1381 (Fed. Cir. 2006) (“[A] prior art reference must be enabling so that the claimed subject matter may be made or used by one skilled in the art.”); Bristol-Myers Squibb Co. v. Ben Venue Labs., Inc., 246 F.3d 1368, 1374 (Fed. Cir. 2001) (“To anticipate, the reference must also enable one of skill in the art to make and use the claimed invention.”). Taken out of context, these formulations of our § 102 enablement standard arguably support a use or utility requirement divorced from any “make” requirement. A thorough reading of our case law, however, makes clear that a reference need disclose no independent use or utility to anticipate a claim under § 102. E.g., Novo Nordisk Pharms., Inc. v. Bio-Tech. Gen. Corp., 424 F.3d 1347, 1355 (Fed. Cir. 2005) (“The standard for enablement of a prior art reference for purposes of anticipation under [§] 102 differs from the enablement standard under 35 U.S.C. § 112.”); Rasmusson v. SmithKline Beecham Corp., 413 F.3d 1318, 1326 (Fed. Cir. 2005) (“[A] prior art reference need not demonstrate utility in order to serve as an anticipating reference under [§] 102.”); In re Hafner, 410 F.2d 1403, 1405 (CCPA 1969) (“[Section] 112 provides that the specification must enable one skilled in the art to ‘use’ the invention whereas § 102 makes no such requirement as to an anticipatory disclosure.”)."

Gleave argued as if the prior art must satisfy the "specific, substantial, and credible" standard of utility, so that the failure to disclose which oligos were functional as antisense molecules would negate anticipation. Again, the court said this is not the standard.

Whether we can decide that the antisense oligonucleotides not disclosed in the cited art had an intrinsic utility isn't the point, and wasn't how the court addressed the question.

You are right that Gleave treated the cited art as being nothing more than ink on a page. In that, of course, they were completely wrong.

Thanks for the comment.

Dear Frank:

There were dependent claims that recited specific oligonucleotides by nucleic acid sequence. These oligos were not expressly disclosed in the cited art; however, some of those 15-mer sense oligos would hybridize to the antisense oligos Gleave's application expressly disclosed.

How I think this decision does not square with chemical patent pracice regarding the species claims is that it is settled law that a later-filed claim to a species encompassed by a generic chemical formula is not anticipated unless the specific combination of substituents comprising the species are expressly recited in the prior art genus. Substitute "nucleotide" for "substituent" and you will see my issue.

Thanks for the comment.

"These oligos were not expressly disclosed in the cited art"

This is hair splitting about the definition of "express". Your chemical species are fine, Kevin.

Dear Frank:

I know the chemical species are fine; why aren't the oligonucleotide species?

The difference is sequence complementarity. That is certainly a position one can take, and one the court did take, although it didn't expressly say so. It just treated the fact of sequence complementarity, combined with prior art disclosure of the sense 15-mers, the degree of overlap and the routine nature of oligonucleotide synthesis, to find the antisense species claims, as well as the genus claim, to be anticipated.

Thanks for the comment.

"Gleave argued as if the prior art must satisfy the "specific, substantial, and credible" standard of utility, so that the failure to disclose which oligos were functional as antisense molecules would negate anticipation. Again, the court said this is not the standard."

And it surely isn't. Gleave's argument was d.o.a. from numerous perspectives.

Ah, Rasmussen! I am very glad to see it has been brought fully back to life. I thought the case had been muzzled last fall or winter by another anticipation/enablement case whose name I can't remember. Perhaps the claims in that other case were method claims?

In any event, whether you characterize the utility requirement as "non-existent" or "so low that any trivial utility will suffice" is irrelevant, as a practical matter. You didn't overstate the holding of this case. I understated the holdings in the previous cases.

"It just treated the fact of sequence complementarity, combined with prior art disclosure of the sense 15-mers, the degree of overlap and the routine nature of oligonucleotide synthesis, to find the antisense species claims, as well as the genus claim, to be anticipated. "

[shrugs]

This is the result I would expect. We had a case where somebody filed an application with 6000+ sequences and no information about actual functions of these sequences, and yet one of them was identical to the coding sequence we discovered. We reviewed (Schering Corp. v. Geneva Pharm., Inc., 339 F.3d 1373, 1380–81 (Fed. Cir. 2003) and resigned ourselves to method of use claims. This was in 2006/early 2007.

Dear Smallfry:

Yes, but remember the Wraight reference disclosed not one antisense sequence - zero. That is the point: the CAFC affirmed a 102 rejection when the prior art did not disclose the claimed antisense species.

Now, I know that the skilled worker would have understood the principles of complementarity, but that isn't the point - either 102 is a bright-line rule or it isn't. I think there would be much less talk about this decision had it been based on 103 (but then additional considerations would have been in play and perhaps the court would not have been able to sustain the rejection).

Thanks for the comment.

Dear Frank:

That's an argument?

"Yes, but remember the Wraight reference disclosed not one antisense sequence - zero. That is the point: the CAFC affirmed a 102 rejection when the prior art did not disclose the claimed antisense species."

Kevin, of all the weaknesses in this case, that is the weakest weakness to point out.

I agree with you that there is a bit of loosey goosiness in the decision. But it's not what you point out. I agree fully with a reading of Wraight that it discloses every 15 mer sense AND antisense sequence "expressly." The language in Wraight is more than sufficient to justify that.

The loosey goosey part is where the court takes it further and uses Wraight to *anticipate* sequences of different lengths, e.g., 20 mers. that aren't disclosed. That should have been dealt with on an obviousness basis, at least here (I admit I haven't read Wraight and for all I know there is more teaching in Wraight than was quoted by the court -- they indicate as much in a footnote).

As always, the question is how much of the case is dicta. I don't think the case is a holding that complementary antisense sequences are anticipated in every instance where a gene is disclosed and a sentence is included in the case that "antisense molecules could be made to target the gene."

I agree it comes close to that, but there is enough precatory language in the decision to justify a narrower reading.

Gleave got what was coming to him/her, I'm afraid. But I'm skeptical that it's a death knell yet for all biotech compositions based on complementary sequences.

Is it a taste of things to come, however (i.e., Kubin)?

"Yes, but remember the Wraight reference disclosed not one antisense sequence - zero. That is the point: the CAFC affirmed a 102 rejection when the prior art did not disclose the claimed antisense species."
...
"The loosey goosey part is where the court takes it further and uses Wraight to *anticipate* sequences of different lengths, e.g., 20 mers. that aren't disclosed."

The Board made the anticipation finding. The CAFC reviewed the legal questions that the applicant raised. I bet if you check the briefs, you'll find that the applicant did not dispute the details of Wraight on appeal, other than the fact that it was an unspecific list. The court barely talked about what exact sequences were claimed and were in Wraight. It's a good bet that the issue wasn't argued.

Dear Frank:

Well, we know the Kubin answer, don't we? More on that Sunday night.

There are, as always, two aspects: whether the case was properly decided for the parties, and the effects it may have on the rest of us. Gleave may have gotten what s/he deserved (including what was argued in the briefs, as Gregg posits). My point was, first, that this is not an anticipation case but an obviousness one, and second that this case will be used (by examiners and infringers' counsel) precisely for the proposition that "every antisense is anticipated by a sequence + the magic words 'antisense'." I just think this is inconsistent with chemical patent practice and how these issues have been handled in the past. If the Court wants to make new law, I'd prefer they would make it clearly.

Thanks for the comment.

Dear Gregg:

Actually, Gleave argued before the Board that the combination of "gene sequence + the word 'antisense'" should not anticipate, and that the mere mechanical recitation of a sequential list of all 15-mer sense oligos should not change the conclusion. The Examiner took the position before the Board that the existence of 5 15-mers that overlapped the elected antisense species anticipated, and the Board affirmed.

I think the record shows that the PTO, at least, knew exactly what it was doing - making a factual determination (harder to overturn on appeal; Zurko, Gartside) on anticipation, using something that amounts to a bright line rule. I'm just not sure this is consistent with established practice, or that the affirmance by the CAFC is not the right result.

Thanks for the comment.

W'aal, just a lil ole biologist here wanting to get the science right first. I believe evolution has played a signficant role in shaping the nucleotide sequences and (novel?)p-chem processes shape the small molecule racemates. Thank you very much.

Dear JC:

From one old biologist to an ole one, you are certainly correct - evolution has played a major part in shaping nucleotide sequences.

But the only way we know that is from the 30,000 foot level of the HGP, which made it pretty obvious, and from sequence comparisons in multigene families. In Gleave, the PTO and the CAFC said that the existence of a list of 15-mer sense oligos anticipated the specific antisense oligos claimed by the applicants. With all due respect to the CAFC, horse hockey.

Thanks for the comment.

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